Nope... I could be wrong on which handloaded ammo, and the actual stats, but pretty much all the types were comparable to the AP or HP real versions, and the one's I checked seemed like lesser versions of the genuine store bought ones.
I can't say for sure about weapon degrading either, but I have the built to destroy perk, only shoot hand loads and have no problem maintaining my weapons.
As far as advantages/disadvantages go, I use hand load .308 and .44 mag swc...
.308 hand load is a compromise between HP and normal rounds (same DT specs + 50% more damage), and from experience, I can say they work great on deathclaws.
I don't know specs on .44 mag swc, but from experience they do good damage against armored foes... (there's no AP version of the .44 mag)
I really wish someone could produce definitive specs...
EDIT:
according to the wiki 45-70 gov't swc hand loads do DAM x 1.20, DT -6.00, so specs for .44 mag swc are probably similar.