If you had ever been in a proper, professional studio. You would know that protools, and logic users are well used to the idea of having external units hanging off the side of their mac. Heck my uni studio (upwards of £10mill spent on the entire complex) had 4 studios with mixers in each, a Mac Pro, and protools hd24 boxes hooked up into the PCI expansion ports, with some old serial connection (can't remember the name off the top of my head)
I am more than certain avid/digidesign are working with apple, and designing a new system which goes like the wind via TB2.
Avid, and protools have become synomonous with apple n mac ever since the dawn of time pretty much, so there will be changes down the line for all that kinda gear
In my mind I don't get the big fuss, there was a reason some clever soul invented cable ties, tape, n cable holders.
It's not like you particularly need access to the cards etc when everything is set up (I rarely have to go traipsing around my rather modular Mac mini studio recording rig in my bedroom.
If you are convinced that the cards are gonna become that much of an eyesore, drill some holes, n ventilation into a drawer under your desk, place external units in drawer, or some other enclosure (rack mount or otherwise, make it sound proof n cooled blah di blah) job done.
Heck if you want it done proper, you can situate the external devices some 10m away if I remember the spec of thunderbolt 2 correctly.
Sometimes change is necessary, I see this change as a good one, one that is no doubt causing headaches for quite a few PC OEMS the world over, on how to counteract this rather large blow to the market. Having said all that, there is no doubt it's a risky change. I can see it paying off
Whoops, long post, maaahhhh bad