Yes. Pinch hitters are based on the pinch-hit hierarchy found in the Manager's Office. When the Sim Manager looks at the inning, the score, the runners on base, the need for power versus contact hitting, and the opposing pitcher to decide that a pinch-hitter is necessary, it will review the Hierarchy to determine whom from the bench should come in in the situation. The player who is highest on the list for the situation will bat. Of course, the manager also checks to make sure this potential replacement is actually a better hitter than the incumbent; if not, the manager will opt not to pinch-hit.
You can also control whether individual players are pinch-hit for by checking the Pinch Hit box in their Advanced Hitting Settings.