I don't think they would be there if it wasn't safe
OnyX does tell you to make sure your computer's backed up before you do anything, however every time I've deleted my caches in OnyX I haven't had any problems (I clean them a lot - I'm a freak about that).
You can remove practically any cache in the system and it will be rebuilt after reboot. I know for a fact that you can safely clear out ANY of the caches from within Onyx and have no odd side effects, if you reboot when it tells you to.