Hello,
Disabling cloud saves doesn't affect your local save files. It shouldn't affect your existing cloud save files either. It should just prevent syncing the saves from that point on and nothing else. To be safe, it would be best to first download a backup of your cloud saves from the Extras tab of the game in question.
If you don't play the same games on multiple computers, then I don't think cloud saves are worth the hassle. I disabled the feature ages ago and I don't miss it at all.
You can selectively delete existing cloud saves below:
https://www.gog.com/account/cloud-saves/page/1