"There seems to be a trend toward high quality mic pre-amps with A/D. Most units use analog limiting just prior to conversion to maximize signal level (and apparently bit depth?) without overloading the converter. When these are used in an all digital MDM/digital mixer setup, should the mic preamp be the master clock, following the signal flow, or can the MDM be the master clock?"

I see two questions here.

1) What about these limiters on the digital preamps? What are they for and how should they be used?

Conventional wisdom in digital recording is that you want the highest signal level you can get prior to A/D conversion to maximize your bit depth. So yes, the limiters and compressors built into many preamps and/or A/D converters are mainly addressing this concern. And they are handy, especially when one is working with unpredictable material (who knows when that singer is going to blast away and cause you to have irreparable distortion on an otherwise excellent take). Different engineers have varied opinions about how (or if) these limiters should be used. In a 24-bit system you have plenty of headroom. In fact 24 bits represent more dynamic range than any of the analog electronics in your chain are capable of! So the truth is that, unlike the old 16-bit days, you don't really have to worry about slamming your levels all the way to the top all the time. Granted, digital signals (even 24-bit ones) will have slightly more distortion or non-linearity at lower levels, but as long as you have reasonably good levels 24 bits is enough to get the job done without agonizing over it. This means you can very easily get away without using limiters on the front end and still end up with a very clean, fully dynamic signal. If you are working with 16-bit technology you need to be more rigorous about maximizing your levels, and the limiters do make that a lot easier.

It also makes a difference if you are recording signals that will be mixed together later. If you have 24 tracks of high level 24-bit signals and you have to mix them down to a stereo pair you are going to be turning them down as you combine them anyway. If the 24 tracks are all recorded at a slightly lower level you really aren't likely to lose much by the time they get mixed together (this also depends on the internal resolution of the mixer). We'll get a lot more into all this minutiae another time. As for your limiters, techniques will vary, but most engineers try to use them as little as possible. They want to capture the source as accurately as possible and apply processing later when they can control it in the context of the mix.

2) Should the word clock come from the source (the preamp in this case) or somewhere else?

The answer to this depends at a practical level on what is available. Many preamps with digital outputs cannot clock to an external source. In those cases your choice is made for you. If the preamp can sync to external clock then you have to weigh your options. It is always recommended that all of your equipment by synced to one clock source, and that source should be the most stable clock in your studio. If that clock comes from a preamp, then use it all the time. If it comes from the mixer, then slave the preamp to that. There's no reason why the clock source has to follow the signal path. You just want to use the best clock all the time.