Using a standard WAD editing tool like XWE you can "clean up" your WAD, but there is little to no wasted space on the official IWAD. I just ran a test on a copy of the IWAD directly from the Doom collectors edition disk, and gained ~500 bytes. Not much of a gain I'm afraid. Also, XWE doesn't want to "clean up" IWADs for whatever reason, so I had to get a hex editor out and change it into a PWAD, then change it back when i'd finished. WinTex may not have this in I don't know. WADs are not compressed at all AFAIK (from what I've read in the "Unofficial Doom Specs" documentation). They are like zip archives or whatever in that they are essentially a directory themselves, but they do not have compression like zip files can. Sorry...
EDIT: Just looked at that cleanwad tool. Nice! It cleans it up better than XWE (judging by those stats in the readme file) but it changes the WAD a lot, wheras XWE just removes "wasted" space. Neat tool! Saves a whole Mb for Doom.wad...