Just ran a test here and what I'm seeing is not what is presented.
I did the following:

1. Backed up my BB using Desktop Manager.
2. Ran MaxMem and removed VAD, MDS (I'm not on a BES), Media, and 2 of the default Themes (I actualy use the Today theme occasionally).
3. Did a battery pull/reset.
4. Restored the backup I initially made.
5. Did a battery pull/reset.

Everything that was removed by MaxMem DID NOT return with the restore. Maybe I did something wrong with the backup/restore, but not that I can see.

It's really no big deal to me, I didn't use any of the stuff that got removed. Just a heads up to those that are messing around that may delete something they actually need.