Personally I would be very surprised if the head on the 9890/7990 is any different than the head on the 9900/7900. You just don't have the orange and black lines running to the head. Might be wrong, having never seen a parts break out.
To answer your questions, no nothing has changed, no different hardware or firmware, at least in U.S. for over a 1 year now. I also don't think that the heads have seen any changes.
Yes, they can and will "clog", however many of the "clogs" are not what I think traditional "clogs", instead they are failures of the ink delivery system. Either the Pizeo nozzle at the head or the electronics behind it. This was very clear in the damage Eric G's printer had, when they finally tore open the head and found nothing visually wrong, even under intense magnification.
Total or 1/2 blockages of LLK, PK, and other inks is common especially after a PK to MK or MK to PK switch and I don't think the lose of 1/2 of a nozzle pattern is a "clog", way too much material would be involved. This is something else. More than likely new units may have newer hardware that addresses this, as such non official upgrades are common in this type of equipment. In large equipment it's termed a EC change and most times will roll back to earlier units, however Epson doesn't do this.
If you purchased a "new" 7990 that wasn't a warehouse sitter for 6 months, odds are you have some newer EC's in it. However I have not seen anything from Epson that addresses this issue of losing a full channel after the ink swaps (PK MK). Most times with my 9900 it happens after about 2 prints which does point to an air issue somewhere in the system. Only fix I have for it is, Power off, come back up in maintenance mode, and run a CL1 or CL2 on the effected channel pair. This still takes a lot less ink than doing it from the normal mode as you only have 2 settings.
In 3 years, I have yet to need more than a CL3 and it only once. I have never had to run the stronger cleaning cycle. Repeated strong cleaning cycles, more than likely do electrical damage to the Piezo head, more than likely due to heat build up.
Epson's need to be run, daily, or at least every 3rd day. Leaving a unit off for extended periods will lead to "clog" issues.
My print work commercially comes in batches, so when I am not running a large job, I still run prints, mainly a color test pattern to move ink through the system.
If you are not in a daily print workflow, the Canon system makes more sense, and looking back, I wish I had invested in the 8400, but my 9900 was a field replacement offer from Epson after 3 failed 9880 replacements. So I stayed with Epson.
Older Epson heads, i.e. 7800, 9880, family are much easily to run in a non-daily workflow. I can leave my 7800 off for a month, power it back on find a few clogs, then clean the wiper, run a couple of cleaning cycles from the LCD and I am good to go. Not true with the 9900 as it needs IMO more daily attention.
Results are great. If you make the investment, buy the 2 year warranty extension and just don't worry for the next 3 years, as Epson will make it right as long as the unit is under warranty. May take a few tries, but they will get it right.
Paul