Can too many ffmpeg encodes at once cause loss of quality?
This is a very broad questions so let me try to answer it in a general sense.

Yes, it is more likely for corrupted files to appear when encoding more files. It is only more likely by a very thin margin though, so using a batch-render-queue is not something to "not do" - in fact, many big budget productions use render-queues to render many many sequences one after another, and I personally wouldn't demotivate you from doing it. However, encoding to mp4 (I assume h.264) always comes with compression, meaning that the file will be lossy and not as good as the original. The CPU being at 100% shouldn't cause any problems though if you didn't overclock your cpu or tinkered with the flags from within ffmpeg (which I assume you didn't do).