When putting armor on wither skeletons, the armor is invisible but it is affecting the mob (takes longer to kill, etc). Same issue when wither skeleton was given a bow. Endermen holding any items that aren't blocks also have the items invisible but they are still there (gave enderman a diamond sword to test and it gave the sword but it was invisible. I know this because when provoked, the enderman one-hit killed me when they normally take half your health.) I would assume this issue applies to other mobs as well besides wither skeletons and endermen (had a vindicator hold a totem in the same hand he was holding an axe in)