I would not want to swim among the American Pondweed either. Yuck. Yes, if you don't like cooler water that is a problem, because best time to attack it is Spring emergence. It must be rooting in a pretty dense bottom like clay instead of muck. Another problem. If you are using a systemic it should kills the entire plant all the way down to the roots. Depending on how much active ingrediant sticks to the leaves is how long it takes. But you should be back to square one pulling out the dead material instead of live, which I why I just pull it out live if I can.
I lake mower curly leaf pondweed, and rake it out. I also clear out swimming beaches and surface areas. Most plants I mow or pull in the Summer do not grow back very well. If I get at the root structure they don't at all. I'm even pulling up coontal which has no root structure but anchors in the muck and mowing it. Even the material I got back a few months ago did not grow back to much of any degree. I think you need to clear out the swimming holes and eradicate there completely. You have to kill the roots and clear it out of the pond, everywhere you don't want it. It normally is not a fast spreader, in fact, it is usually slower than many species. Wheter you hand pull or spot treat with herbicide, get the plants out and reduce the nutrients. That is probably the source of many of your problems.
