It's okay to do mass editing projects as long as you do it carefully:
- Make sure your plan is clearly an improvement before you start.
- Don't bump more than a few (let's say 3) to the front page at any given time. (Editing all answers on a question at the same time still only bumps one question.)
- Be sure to fix other things in the posts as you're editing.
I think this seems like a small but reasonable improvement, if done carefully. There are a couple concerns:
- Some links may deliberately point at an older printing of a card, while the automatic link always points at the newest.
- Some auto links don't actually work, including apparently card names that are substrings of another card's name. Make sure the new link actually works.
Outside of those corner cases, I don't think old gatherer links have broken in general, but replacing them with
[mtg:...] links does prevent breakage in the future. It also standardizes the way the links are presented.
So I'd say go for it if you want, with the above things in mind. The slow rate means that organizing help isn't exactly necessary, but encouraging people to change links if they're already editing something else seems good. Or if it all seems like too much trouble at that point, just forget about mass editing and only edit the posts you come across otherwise.