Sounds like they just need more exercise to me!
If Jackson doesn't get enough exercise, is when he starts to bother me in the evenings - finding things to chew, whining for me to play, etc, etc, and he's almost 4yrs old.
Even today, I took him on an hour walk along park trails with his 50ft leash so he had lots of room to run & explore, we got home and he still wasn't tired, so we went outside and did 30 more minutes of frisbee and 15 minutes of uphill running and he still could've kept going... but he's not necessarily the norm, he could keep going and going
But in general, I believe EVERY dog should get at least 30 minutes - 1 hour of outdoor time per day, weather depending of course.
I think that in answer to your question, crates are fine at night - it's just a matter of how you use them or abuse them. I personally wouldn't want to be using a crate during both the day and the night but that's just me. I say they just need a bit more exercise and training. Exercise cures a lot of small behavioral problems.