I've used them very little and have not experience any problems personally but that's probably because I avoid using them when ever possible. However I've hear countless stories and have seen examples when vehicle roof top installations bend the roof metal, broke when the antenna struck something, leaked water, rusted out, came lose etc.
Installer issues.
I've got an F-350 4x4 with an NMO dead center in the aluminum body roof. On there I have a Larsen NMO 1/4 wave VHF wide band. Last year I was in Las Vegas for a conference and forgot about the antenna. Drove into a parking garage and hit it hard. While those antennas have a spring at the base, they are pretty stiff. The whip material is much thicker than the standard NMO's. Due to a bunch of cars behind me, I couldn't stop to remove the antenna. Just had to deal with the noise.
When I was able to stop, the spring had taken a permanent bend to the rear. The NMO base was still fully intact, including the aluminum roof it was mounted on.
When I got home, I ordered just the spring part, and replaced it. No damage to the truck or the rest of the antenna.
Damaging the roof top is possible, but it's usually done by someone doing a poor job of installing it.
Leaking/rusting is another installer issue. Failure to make the right sized hole can cause that. Failure to properly install and lube the included o-ring at the base. Failure to properly maintain it. All things that require a bit of work, but certainly not hard to do.
The coax usally has to make a very sharp 90 degree bend immediately at the NMO base.
This tells me that you haven't installed one before in a roof mount. The NMO design has the coaxial cable leaving the base at a 90º angle.
They seem to be prone to cross threading,
Sounds like the typical Tram/Browning/Cheap Chinese Crap. They use soft materials on the bases and the antenna coils. They'll cross thread if you don't start them correctly. A good name brand (Larsen, Laird, Antennex, MaxRad, etc) will not do that. Important part is to not try and save a few bucks by using the cheap crap.
the center pin connection isn't 100% reliable and not consistent even though it's supposed to be an industry standard.
I've seen that on a few installs. Sometimes it's due to the installer not using a mount designed for the roof thickness. Sometimes it's a poorly designed antenna coil.
You are correct that there doesn't seem to be a standard to address this, but it's also something that would be checked easily by using an SWR meter or antenna analyzer after the installation.
Some antennas have a sping loaded solid brass center pin, while others use a cheap thing flat spring tab.
"Pogo-Pin". Done right, those can work. Done wrong, they crap out. Motorola 800MHz antennas from the 1990's used a pogo pin that was sheer and utter crap. Those failed very frequently. A really poor design.
Newer ones seem to be much better.
The tab issue usually is from the wrong thickness mount installed and someone trying to bend the tab down to make up for it. Done incorrectly, they will break. If the install is done correctly, it's not an issue.
The few ground plane conversion kits I've seen do not have an adaquite diameter to make a good seal with the O-ring in the typical NMO antenna.
Yes, and again someone that pays attention to what they are doing will catch this. Using a base conversion kit is good for a temporary installation. Using them as a permanent solution, well, that's an installer doing his/her best to get out of doing a proper job.