For speed runs, any random encounters at all is generally a bad idea. I remember when I did my EXII run, the only two levels in the game I allowed myself even one random encounter were Oeilvert and Memoria, simply because I was starting to pull my hair out after a hundred resets in Oeilvert, and Memoria I let myself relax a bit since my time was pretty good and I knew I had the EXII in the bag at that point.

But yeah, if you don't like encounters, it's perfectly possible to get through almost any area in the game without even getting into one, if you're willing to reset a few times. Random encounters in FFIX are actually notoriously low. Or at least notoriously random in their frequency. Also, battles tend to stand out more when you do get into them because battles in FFIX are so slooooooooow.