Generally fragmentation is not too bad with FFS. Most defrag programs are old and could cause problems for little gain from defragging. If you are worried about HD performance or fragmentation then I would recommend you try PFS 3 which is better at both...
http://aminet.net/disk/misc/PFS3_53.lha http://aminet.net/disk/misc/PFS3_53.readmeDitto. Regarding cooling fans, only time I'd ever bugger with that is if you have an overclocked 030 or an 040/060 and/or an Indivision AGA installed. Otherwise, leave it alone unless you feel lots of heat coming through the case.
It's good to have a cooling fan for almost any 68040 IMHO. The 68030 and 68060 don't need it unless overclocked.
