I might be wrong in several places, so please correct me if I am.
The Steam version of Oblivion had the main .exe encrypted, so that several mod components / tools (eg. Oblivion Script Extender) could not function with it, thus making it impossible to use a few mods with this version.
1. Will this also be the case in Skyrim?
2. Does someone here has experience with installing mods with the Steam version of Oblivion, and if so, how goes it? Is it harder / easier than with the physical copy? Does one use tools like OMM, or is everything handled from within the Steam application?
i don't know where you got your information from but OBSE works just fine with the Steam installation.
I have around 150+ mods installed, including some that only work with OBSE, such as OBGEv2, ENBSeries Shaders and the major overhaul mods such as OOO, MMM, Frans, FCOM.
The utilities I use are BOSS, Wrye Bash, OBMM, OBSE, Oblivion Crash Prevention System, Fast Exit
There are only two different steps for Steam users
(1) 4GB patch uses the steam version .dll file
(2) When installing Wrye Bash you need use your text editor to correct the default file paths in the bash_default.ini file and save the file as bash.ini
That's all you need to do differently AFAIK
Here is a list of the mods I have running on my Steam installation of Oblivion:
	Spoiler 	Active Mod Files:00  Oblivion.esm01  Silgrad_Tower.esm  [Version 3.36]02  Jog_X_Mod.esm03  Francesco's Leveled Creatures-Items Mod.esm04  Francesco's Optional New Items Add-On.esm05  Cobl Main.esm  [Version 1.72]06  Oscuro's_Oblivion_Overhaul.esm  [Version 1.34]07  Mart's Monster Mod.esm  [Version 3.7b3p3]08  FCOM_Convergence.esm  [Version 0.9.9MB3]09  Armamentarium.esm0A  Artifacts.esm0B  Better Cities Resources.esm0C  Cobl - NPCDiversity - TNR Merge.esp  [Version 9.3EV-D]0D  Unofficial Oblivion Patch.esp  [Version 3.3.3]0E  DLCShiveringIsles.esp0F  Unofficial Shivering Isles Patch.esp  [Version 1.4.0]10  FCOM_FrancescosItemsAddOn.esp  [Version 0.9.9]11  FCOM_FrancescosNamedBosses.esp  [Version 0.9.9]12  Symphony of Violence.esp13  Atmospheric Oblivion.esp14  WindowLightingSystem.esp15  Enhanced Economy.esp  [Version 5.1]16  FF_Real_Thirst.esp17  DLCOrrery.esp18  DLCOrrery - Unofficial Patch.esp  [Version 1.0.4]19  DLCVileLair.esp1A  DLCVileLair - Unofficial Patch.esp  [Version 1.0.6]1B  DLCMehrunesRazor.esp1C  DLCMehrunesRazor - Unofficial Patch.esp  [Version 1.0.5]1D  DLCSpellTomes.esp1E  DLCSpellTomes - Unofficial Patch.esp  [Version 1.0.1]1F  ArmamentariumVendors.esp20  SnakeArmor.esp21  trfjChronoStaff.esp22  XSPipeMod.esp  [Version 1.2]23  DLCThievesDen.esp24  DLCThievesDen - Unofficial Patch.esp  [Version 1.0.5]25  DLCThievesDen - Unofficial Patch - SSSB.esp  [Version 1.0.4]26  Cobl Glue.esp  [Version 1.72]27  Cobl Si.esp  [Version 1.63]++  Cobl Tweaks.esp  [Version 1.44]28  Bob's Armory Oblivion.esp29  FCOM_BobsArmory.esp  [Version 0.9.9]2A  Oblivion WarCry EV.esp2B  FCOM_WarCryNoSpawn.esp  [Version 0.9.9]2C  Oscuro's_Oblivion_Overhaul.esp  [Version 1.34]2D  Mart's Monster Mod - Additional Enemy NPC Vars.esp  [Version 3.7b3p3]2E  FCOM_Convergence.esp  [Version 0.9.9Mb3]2F  FCOM_RealSwords.esp  [Version 0.9.9]30  FCOM_DurabilityAndDamage.esp  [Version 0.9.9]31  FCOM_SpawnRatesSlightlyReduced.esp  [Version 0.9.9MB3]32  Mart's Monster Mod - More Wilderness Life.esp  [Version 3.7b3p3]33  FCOM_LessRats.esp  [Version 0.9.9]34  FCOM_LessReaversInGates.esp  [Version 0.9.9]35  Mart's Monster Mod - Extra Wounding.esp  [Version 3.7b3p3]36  Mart's Monster Mod - Looting NPCs & Creatures.esp  [Version 3.7b3p3]37  Mart's Monster Mod - Less Reavers.esp  [Version 3.7b3p3]38  Mart's Monster Mod - Zombies for Body Meshes.esp  [Version 3.7b3p3]39  Mart's Monster Mod - Dungeons of MMM.esp  [Version 3.7b3p3]3A  Mart's Monster Mod - Gems & Gem Dust.esp  [Version 3.7b3p3]3B  Mart's Monster Mod - Hunting & Crafting.esp  [Version 3.7b3p3]3C  Mart's Monster Mod - Diverse WaterLife.esp  [Version 3.7b3p3f]3D  Mart's Monster Mod - Slof Horses Complete.esp  [Version 3.7b3p3]3E  Mart's Monster Mod - Diverse Runeskulls Loot G&GD.esp  [Version 3.7b3p3]3F  FCOM_DiverseGuardUnity.esp  [Version 0.9.9]40  FCOM_BobsGuardUnity.esp  [Version 0.9.9]41  FCOM_HungersUnitySI.esp  [Version 0.9.9]42  FCOM_FriendlierFactions.esp  [Version 0.9.9]43  FCOM_MoreRandomSpawns.esp  [Version 0.9.9]44  FCOM_MoreRandomItems.esp  [Version 0.9.9]45  Mart's Monster Mod - Shivering Isles.esp  [Version 3.7b3p3]46  OOO-WaterFish.esp  [Version 1.34]47  300_Artifacts.esp48  Artifacts.esp49  hackdirtabyss.esp4A  thievery.esp4B  thievery - EE patch.esp  [Version 4.2]4C  DLCBattlehornCastle.esp4D  DLCBattlehornCastle - Unofficial Patch.esp  [Version 1.0.4]4E  DLCFrostcrag.esp4F  DLCFrostcrag - Unofficial Patch.esp  [Version 1.0.5]50  Knights.esp51  Knights - Unofficial Patch.esp  [Version 1.1]52  FCOM_Knights.esp  [Version 0.9.9Mb3]53  xuldarkforest.esp  [Version 1.0.5]54  xulStendarrValley.esp  [Version 1.2.2]55  xulTheHeath.esp56  XulEntiusGorge.esp57  xulFallenleafEverglade.esp  [Version 1.3.1]58  xulColovianHighlands_EV.esp  [Version 1.2.1]59  xulChorrolHinterland.esp  [Version 1.2.2]5A  xulBravilBarrowfields.esp  [Version 1.3.2]5B  xulLushWoodlands.esp  [Version 1.3.1]5C  xulAncientYews.esp  [Version 1.4.3]5D  xulCloudtopMountains.esp  [Version 1.0.3]5E  xulArriusCreek.esp  [Version 1.1.3]5F  xulPatch_AY_AC.esp  [Version 1.1]60  xulPantherRiver.esp61  xulRiverEthe.esp  [Version 1.0.2]62  xulBrenaRiverRavine.esp  [Version 1.1]63  xulImperialIsle.esp  [Version 1.6.6]64  xulBlackwoodForest.esp  [Version 1.1.0]65  xulCheydinhalFalls.esp  [Version 1.0.1]66  xulAspenWood.esp  [Version 1.0.2]67  xulSkingradOutskirts.esp  [Version 1.0.1]68  xulSnowdale.esp  [Version 1.0]69  Better Cities - House price patch.esp  [Version 1.0]6A  RealSleepExtended.esp  [Version 2.5]6B  Ashes to Ashes.esp  [Version 1.0]6C  Vampire Aging Disabled 2 XYoung.esp6D  bgMagicEV.esp  [Version 1.7EV]++  SM_UnlockSpells.esp  [Version 0.70]6E  Moonshadow Elves - Sc.esp6F  1em_Vilja.esp70  _Ren_BeautyPack_full.esp71  _Ren_BeautyPack_onlyhairs.esp72  tkHairPack01.esp73  Cobl Races.esp  [Version 1.52]74  ElaborateEyes.esp75  bgMagicEVStartspells.esp  [Version 1.68EV]76  bgMagicBonus.esp  [Version 1.7EV]77  bgMagicEVAddEnVar.esp  [Version 1.68EV]78  bgMagicAlchemy.esp  [Version 1.57]79  SupremeMagicka.esp  [Version 0.90]7A  SM_OOO.esp  [Version 0.89]7B  SM_MMM.esp  [Version 0.89]7C  SM_COBL.esp  [Version 0.86]7D  SM_ShiveringIsles.esp  [Version 0.86]7E  SM_EnchantStaff.esp  [Version 0.80]7F  SM_Scrolls.esp  [Version 0.84]80  SM_DLCSpellTome.esp  [Version 0.80]81  SM_VanillaSpells.esp  [Version 0.86]82  bgMagicSpellTomes_for_WryeBash.esp  [Version 1.68EV]83  bgMagicEVPaperChase.esp  [Version 1.68EV]84  bgMagicEV_Conjuration_for_Supreme_Magicka.esp  [Version 1.5]85  bgMagicEVShader.esp  [Version 1.7EV]86  bgMagicShaderLifeDetect.esp  [Version 1.68]87  bgMagicLightningbolt.esp88  ElaborateEyes-RensBeautyPackFull.esp89  HTFpcb Extended.esp8A  ElaborateEyes-RensBeautyPackHairsOnly.esp8B  FCOM_Archery.esp  [Version 0.9.9]8C  Oblivion Graphics Extender Support.esp  [Version 0.3]8D  Real Hunger, Cobl.esp  [Version 1.6.1]++  Cobl Filter Late MERGE ONLY.esp  [Version 1.53]8E  FormID Finder4.esp8F  Better Cities Full.esp90  Better Cities .esp91  Better Imperial City.esp92  Better Cities - Unique Landscape Chorrol Hinterland.esp93  Better Cities - Unique Landscape Barrowfields.esp94  Better Cities - COBL.esp  [Version 2.1]95  Better Cities - Thievery.esp96  Better Cities - Unique Landscape Cheydinhal Falls.esp  [Version 4.8.1]97  Better Cities - Unique Landscape Imperial Isle.esp98  Better Cities - Unique Landscape Skingrad Outskirts.esp  [Version 4.8.1]99  TNR ALL RACES FINAL.esp9A  TNR - ShiveringIsles no helms.esp9B  Bashed Patch, 0.esp9C  Duke Patricks - Combat Archery.esp  [Version 5]