Yes, since even on the website on mobile or desktop, you have the 1000 indexing limit. PDS relies on hitting the delete button on each comment/post that's visible. So if you can't see a comment because it's past the 1k limit, then PDS can't see it either and can't delete it.

Now, the changes to the API probably won't. Power Delete Suite is a javascript plugin on the browser and when I look at it, there's no api calls. Rather it just simulates you clicking manually on the edit / delete button of each submission / post.

However, PDS relies on the old dot reddit dot com layout (and goes to there automatically), so it might stop working if we lose old reddit.

The other thing is that I tried PDS and have had a very bad experience with it. Compared to the scripts out there like shreddit, I found PDS to be unreliable (no way to verify it deleted successfully if a rate limit stopped it, also it doesn't save all content and returned a truncated CSV file).