I delete them all the time. What is suppose to happen when you delete them?? My game is acting fine and has never showed a problem with deleting them.
Their old memories (and the ones of sims who met them) are stuck still thinking they exist since the game do not delete sims properly, and from time to time and generation to generation it can cause major problems making the hood unplayable. When you kill them, proper memories are taken care off.
If you never played a hood for long and do not have many genarations, you might have never encounter problems but if you change your play style you will for sure.
As for your question nOmki, you can use "Delphy download organizer" tool to sort your download by category, it can also tell you if you have orphan meshes or recolors and if you have duplicate files. That tool can be found at the MTS2 site. It is a must if you have a lot of downloads.
BTW if you deleted meshes but not the clothes coming along with it (they are like recolors of the mesh), it can explain why you have black and grey bodies since the sim are still trying to use the recolors made with the mesh. Always delete both if you do not wish to have problems. You can simply try to put it into new clothes it should solve the problem but you should still use Delphy's tool so if you deleted many meshes it will find orphans. That will avoid it happening to other sims. Rarely when you delete meshes the recolors coming with it will be deleted, same apply if you delete recolors the mesh won't be deleted.
Usually mesh files will have the word "mesh" include in their file name.