Final Fantasy XIV Database - Ffxivpro.com

Long story short:

You use any software at your own risk. There are no guarantees, no assurance, and nothing is set in stone. The same can be said for FFXI itself as much as the windower.

Proof of this: SE reserves the right to do whatever they want to you, anytime they want, with or without a reason at all. The use of windower is pretty irrelevant overall. If you get in trouble, you compromised yourself one way or another.