I think you see that more in the women's game than in the men's. Little handchecky type fouls can very easily turn into harder fouls or god forbid fighting. I've seen a team shoot a bunch of foul shots one time in a quarter this year though. Its a positive change, but I still prefer the old one and one over 2 shots.
In terms of your last point.......handchecking is the most obvious place where that happens. There are a lot of parts of that rule that I think officials at some levels don't understand. The idea is not to put a quick whistle on a hot stove type play (defender puts hand on offensive player, takes it off, and then puts it back on), which is a foul by rule. The question I think some officials need to ask themselves is this: Does the defender having a hand on the offensive player create some kind of advantage?
As I said officiating can be a tough job, much tougher than most fans realize.
First priority of an official always has to be to keep the game safe and in control. You have some teams that by the players personalities or the way they are coached who tend to come out being more aggressive than the spirit or the letter of the rule book. As you mentioned this kind of play can lead to a hard physical game that has the potential to go over the line into being dangerous.
When I was coaching the hand checking never bothered me unless it turned into grabbing or shoving in a way that would alter the ability of a player to move freely.
There are some officials out there who don't wait to see if the teams are going to be aggressive, they want to establish the idea that they are in charge of the game and tend to call almost anything in the first few minutes of the game as a way of telling everyone to back off. I'm not a fan of these officials but they are out there and as long as they are calling it evenly the players should be able to adjust.
As stated though it does cause more of a problem in halves than quarters. If they blow the whistle 3-4 times in the first few minutes then a team has to play the entire half tentatively to avoid giving up a bunch of free throws. In quarters they need to make it to the quarter break then can go back to playing normal basketball.
The shortage of good officials is something that could end up hurting the game at all levels. We have some guys out there in their 60's who should be retired but there aren't enough young officials to replace them. There are also some officials who frankly aren't very good but again it's them or nobody so they work.
I wonder if the high schools and colleges in Colorado shouldn't do a couple of yearly camps for graduating high school seniors who have a love for the game but aren't good enough to continue as players. Might even set up a scholarship fund to promote interest ($1000 a semester with the requirement that they officiate X number of games at some level be it Jr. High, FR/Soph, AAU, etc.) to get their foot in the door.
Way back I tried to encourage one of my players to go into officiating but I don't think he ever did. He was limited as a player but had an outstanding sense of what was happening on the court and was so emotionally level on the floor it was scary, absolutely nothing ever got to him until he dropped a big smile after a win.