I have both,
I have one system with both OS9 and X and another system running pure X. I have removed most of my classic apps from my dual boot system with little to no incident. You may have to point some files to the OSX version of an app if they were once connected to the classic version. Things like .doc, .mp3, .jpg... you get the idea. If you rip out Acrobat reader classic your .dpf files might complain about it when you try to open it. So.... you just have to point them in the right direction the first time you do it.
I know what you mean when you say you need to make room. My pure OS X system is on a Rev-a iMac with a 4GB drive! It has 192MB RAM and a 466G3 that I put in so it runs ok but... man... 4GB is just too small! OS X is 1.5GB with out the developer stuff!
-evildead