As far as I can tell 916 can fly.
44 creatures can BOTH fly and have acrobatics... meaning 1080 0f 3535 (about 30%) of monsters can fly and/or have acrobatics.
Note that these numbers actually include all monsters that have the word "fly" or "acrobatics" in their stat block, some of which might not actually fly (I didn't go through them all to check). Additionally, some of these (such as the Eladrin Dune Sniper) don't normally have a fly speed, but can gain one by spending an action (a standard action in the Sniper's case) - by the time the monster can spend that action, it is likely too late (the Sniper does also have acrobatics, but other monsters may not). In other words, at most 30% of monsters have either, and the number is probably somewhat lower than that.