You're always at liberty to look at the directory contents for each component of $PATH and decide whether you use the programs therein. If you don't use the programs, the chances are, you won't be hurt by removing the directory from $PATH. If the directory doesn't exist, then you can completely safely remove it.
It is puzzling that the directories show up in your profile and related files. You should check for ~/.profile too. You should also look at material like /etc/profile.
Personally, I consider I am in charge of my PATH. I set it from scratch according to my rules, picking the directories I need. You're not obliged to accept what the system admins set for you, though you should not idly remove PATH components that they've added. But their views on what's desirable may be different from yours.
The only long-term undesirable effect might be that some program you use stops working because it relied on something from the old version of $PATH. So, keep a record of what you had before you started messing with PATH - but don't be afraid to adjust PATH to suit yourself.
