Limestone vs. freestone doesn't come into it that much, other than as a predictor for other things.
Water quality is one. For instance, as TB says, many hatches that Spring Creek historically had, it no longer does. This is common throughout the state. Some bugs (such as sulphers) are more tolerant of water quality issues and thus hung on through some abuse, and as a result, are now much more widespread than some other bugs.
The other big one is physical habitat. Substrate, current, etc. Some bugs thrive in rocky pools, others in rocky riffles, others in gravel, others in silt, etc. Certainly, limestone vs. freestone is correlated with some of those things, but it doesn't cause them, per se. Penns Creek in the canyon, for instance, is a limestoner by water chemistry but the character of the habitat is considered more typical of a freestoner. BFC is a similar situation. But the Letort, well, you won't find the rocky riffle type bugs there. You will find plenty of bugs associated with vegetation, like cressbugs. You'll also find mayflies associated with silt/fine gravel and slow water, like Baetis variety BWO's.