The real pain with the YH100 is the very shallow cup and baffle that folds over the front  -  overall it is a fun process for developing new vocabulary..dB

I didn't get the feeling the YH100 cup is any shallower than the YH1, did you?  They are both too shallow.  Biggest problem with the housing IMO

RD do you think it's a bigger PIA to mod the YH-100 since they don't have the rear opening holes like the HP-1?

The YH100 is definitely the most challenging Yammie to damp and mod IME though the YH1 is a bitch too.  The driver is just a big picky bastard.  I guess the challenge comes from the likelihood that it's got extra issues to deal with that the YH1 doesn't have.  But it's not a terrible place to have ringing like that, I mean compared to some other phones.  If it's not bothersome to you (or desirable as I'm guessing it is to most HF'ers) it does have the crazy man bass. 

I don't think the side vents are a big factor but I can't be sure.  I might drill holes into the back of the cups and see what happens, but it's really time consuming to do neatly and I'm not sure it's worth it. 

3kHz, humm, difficult question because pretty much everything could potential ring there (closed or semi-open acoustic chamber, diaphragm, frame, coupled structural/acoustic mode).

Without seeing the actual design, the quickest way to investigate would be to measure the open air baffled (doesn't need a large baffle, just stick the mic in the near field) driver response. I am not familiar with orthos in general, and the yammy driver in particular so I am close to useless here .

Problem with that is that the drivers need damping to function right, so you might be measuring the lack of damping more than the lack of cups.  But I'd love to see what would happen.  Marv, you're welcome to open them up if you're up for it, let me know and I'll tell you where the screws are.  These orthos are very cool in that the cable is attached to the driver, which is free floating, so you can easily remove the driver and play with it.  Just have to be careful no dust or debris get into the driver, so keep it covered if it's sitting out.