Upon re-enabling the mod, will I regain the items granted to me?
With Skyrim CTDing if I have too many quest mods enabled I want to know if loot I get from them will be removed until I re-enable the mod or if it's gone after it's disabled.

I don't think you will. If you disable the mod and load up a save that previously had it enabled then you will find your items have been removed. If you then save again and re-enable the mod you will find any previously added items are still missing even though the mod is now enabled. However if you load it up with the mod and DO NOT save, close it and reload at a later time with the mod enabled, it will show the items in your inventory.

Its gone forever as soon as you resave without the mod loaded. You need to revert to a save before you removed the mod (and have mod installed) in order to have all your items. Note that all the bugs of a mod are NOT removed from the savegame when you uninstall it, they remain for your continued enjoyment

Yeh, the fact that Skyrim enjoys holding on to old versions of Scripts has caused me know end of troubles when developing my own mods.