Pinch Hitting takes into account a pitchers target and max pitch count, as well as their pull settings and your team Pinch Hit preferences/aggressiveness.
I almost always run teams with unusual pitching staff set ups and never run into issues where I don't have guys available, and I also tend to go WAY light on IP compared to most, rarely drafting more than 1250 IP, and usually staying as close to 1200 as I can. If you're running into issues with guys not being available, it's most likely in the pull settings or their pitch counts, or some combination thereof coupled with your PH aggressiveness.