Also, if I deleted an item of clothing using a custom mesh my sim is still wearing in game, would they just revert to Maxis clothing?
Yes they would. They will choose the next available outfit. Make sure you delete the mesh too, not just the clothes or the sim might be flashing blue.
As for your other question, I am not sure, I think the memories will vanish along with the object but would that corrupt the sim, no idea. I avoid using cc objects using custom memories. You could just back-up your hood, delete the object, load your hood, quit and check if they are still there in SimPe.