There are several reasons above and beyond what was mentioned.
1.) Efficiency. This one was already mentioned in a way, in the form of parasitic loss, etc, but I will put it into even more layman terms. Supers take horsepower to drive them. They result in a net increase in horsepower, but at the cost of adding a BIG load on the engine to do so, and so a loss of fuel efficiency. In an industry where MILLIONS of dollars are made on a difference of one mile per gallon, supers just don't add up. Turbos add (more or less) FREE power to the engine by using scavanged exhaust pulses to drive boost. Net result is BETTER fuel economy and BETTER power.
Just for reference, I understand supers put a parasitic loss of somwhere between 25 and 50 percent on an engine, where a turbo can be as little as 2 to 15 percent (mostly due to exhaust backpressure)
2.) LOAD SENSITIVE BOOSTING. This is a HUGE one that many people miss. A super, being crank driven, makes boost via engine RPM, not via engine load. So, to get maximum boost, you have to be at redline. Diesel engines make peak torque at somewhere around 30 to 50% of redline RPM, so they would only be at 30 to 50% boost in peak torque range. Wnat max boost? You're at redline where the torque has dropped off and you're efficieny sucks! Turbos make boost based on your right foot. More throttle, more boost. You can have maximum boost right in the sweet spot of the torque range, and run your diesel where it wants to be all day long at max power and max boost, not at redline (where we all know diesels don't need or want to be!) Think of a bog cat diesel, which will pull out of 500 RPMs all day long. With a turbo, it can make big boost at that RPM level. With a super, it is barely above atmospheric pressure!
3.) Diesel RPMs are too low. As described above, you would have to overdrive a super on a low RPM diesel to get any sort of boost numbers out of it, and that just increases parasitic loss by giving the super a leverage advantage on the crank.
4.) And finally, THEY DID use superchargers on diesels. on 2-stroke diesels, blowers were an intergral part of the engine design. they wouldn't run without one, because the stroker relied on the blower for intake and exhaust scavanging. But they were never meant to be power adders because at the low RPMs of a diesel, they only made a peak boost of 3 psi!