I know in Oblivion that the steam version was encrypted, preventing some mods such as the script extender. I've heard this will not be the case for Skyrim, but I wanted confirmation before buying the digital version and finding out later on.

No. There were never problems with OBSE and Steam. That was D2D. Also, this should really be in Support or Discussion.

Nope.

Actually, I do recall some initial problems with OBSE and the Steam version of Oblivion when Oblivion was first released on Steam. But Valve listened to modders and players over on the Steam forums and changed the encryption of the Steam version of Oblivion.exe. This coupled with an updated version of OBSE eliminated the issue.