Depends on the mod, but yes, mods are affected by patches, and if not applied carefully, your mods will break. It's a pain, but the best thing to do is compare each file in the patch with the corresponding file in your site with a file comparison program like SourceGear DiffMerge. Use this to ensure you don't overwrite the custom coding of the mod. If your site is live you want to apply this in a development reproduction of your site for testing first. Big pain, but its the only way to ensure see more you don't lose your mods. Even then some mods need to be recoded if the patch significantly changes default code.