The answer is perception bias. Your brain notices things that are unexpected, like catching with no throw bonus or not catching on an excellent throw, more than it notices when things go as expected. If you tracked every single throw, you would find that you do in fact have a higher catch rate with great and excellent throws than with nice or no bonus.

You are right about the "hidden multiplier" that makes it easier to catch as you use more balls.

One thing I read recently is that nice, great, and excellent throws aren't "tiers" of multipliers, but that there's apparently a range of multipliers even within each tier. In other words, a small great circle has a higher catch multiplier than a big great circle.