Assuming you mean a mod that affect theming, the answer is *probably* not, but it depends on a few things, such as what the ROM was designed for and what exactly it's changing (theming has to be done in just a couple framework files). As a general rule, you're probably fine, but make sure the mod is known to be compatible. Do you have an example of something you want to try?

 

Hehe, that's probably due to something else. Those mods wouldn't do that. Did you flash any different kernels or install any new apps recently?