! have seen most of these glitches. But, don't have them now.
As sunnydays says, the moveobjects on cheat can cause problems if you play with it on. Turn it off before resuming play with moveobjects off.
One way of fixing an invisible sim is to send them for a shower. So, I would suggest trying this.
I don't use mods or cc, and you do not say if you do or not. My advice is, if you have this, remove it for the time being.
Do a factory reset. It could fix the problems, it did for me, but, whatever happens, it will do no harm and will speed up your game generally.
Which town are you playing in? Stuck npc sims will cause the type of stuttering and freezing you describe. You can fix this temporarily using resetsim *. For a permanent fix you need to locate and remove the pathing problem which is responsible. For example: Horses can get trapped in the fences around the science laboratory in SV. Use testingcheatsenabled true then enablelotlocking on and remove the fences, or buy the science facility then edit it to remove the fences.
Hope this helps.