Spinning down a drive doesn't power off the electronics -- nor does it cool the drive completely. What it DOES do is let the drive cool down a few degrees and save a bit of power. The drives don't undergo a full thermal cycle, as the electronics are still generating heat -- turning the system OFF will drop the temps a LOT more. There's a difference between a power on/off cycle; and a spinup/spindown cycle -- I agree you would not want to have an excessive number of full power cycles every day. Personally, I NEVER power off the electronics -- my computers are never turned off (nor do I use S3).
Whether you use 15 minutes or 5 hours for your setting, you're not likely to have more than a few spinup/spindown cycles per day in real world usage. If your drives are spun down 95% of the time (i.e. they're only powered up for an average of 72 minutes per day, that means you're only accessing each drive on average once every 4.2 days (since once you access it, it spins for 5 hours). In that case, a 15 minute spindown would make little difference in the number of spinup/spindown cycles -- but would save 4 hrs and 45 minutes of unnecessary spinup time. If you frequently have 30-45 minutes of inactivity during "active" use times, I'd set the spindown to 1 hour.
There's a reason most commercial servers use LOUD, high-volume fans -- to keep the drive temps in the low 30's, as 40+ temps are generally undesirable (although the drives are typically rated to 50 or better (enterprise drives typically to 55). But most UnRAID setups use much lower-volume (and quieter) fans, and will run in the 40's when spinning. While this isn't necessarily "dangerous", it's a good idea to let the temps settle back into the 30's when possible ... and spinning the drives down achieves this easily. My drives typically run 38-40 when highly active; and in the low 30's when spun down.
I agree, however, that as long as your thermals are good, it doesn't really matter if you spin the drives down.