I love the idea in principle, especially as I'm not in a position to donate directly myself. Ideally I'd like to see a modder's helpfulness and willingness to engage with users rewarded as well, but I realise that's almost impossible to measure objectively and you've got enough to be doing.
Off the top of my head though I can see an issue that could be fixed, or at least accounted for (apologies if already addressed).
Doesn't it skew unfairly towards makers of mods for the most popular games? As an example, the most downloaded Companion mod (comparing the same category to be more equitable) for Morrowind (comparatively high on the list of supported games at no.9) has had about 1,500 unique dls. The one for Oblivion (no.5) has had nearly 38,000. For Skyrim (no.1) over ten times that, at around 388,000 uniques. Even though the payout is based on downloads in the last 30 days, those numbers are going to skew similarly I think; probably even more so. That was a flawed example because doesn't take into account how long those mods have been available, but gives a rough idea (similar ratios can be seen just looking at recent mods).
I appreciate it's almost impossible to make a 100% fair system but maybe some sort of maths could be applied to factor in the game's overall popularity and give modders of less popular games a chance to get something significant from the pot?
Something like - take the number of unique downloads for the period for each mod, then divide by the total number of unique downloads for all mods for that game only over the same period, multiplied by (say) 100 to avoid too many 0.xxx numbers (unnecessary step, but handier for this example). This gives a figure that represents the popularity of the mod among nexus users of that specific game. For the sake of this example let's call that figure AP (Andy Points - what an ego eh?). Then use the number of AP to determine the number of DP (and therefore cash etc) each mod gets.
Example using made up (but vaguely plausible) figures for simplicity -
Albert makes a mod for Morrowind which gets 100 uniques in the first period. The total number for the game in that period is 1000.
Brenda makes a similar mod for Oblivion and gets 1000 uniques. Total for the game 10,000.
Chuck makes again a similar mod for Skyrim and gets 10,000 uniques. Total for the game 100,000.
Using your example figures from the FAQ, there are 2 DP to assign per unique. So, (without applying my idea), Albert gets 200 DP, Brenda gets 2000 DP, and Chuck is in the money with 20,000 DP. Each of them gave a similar amount of blood, sweat and tears, and each of them did work that was similarly popular among players of their respective game.
Using my idea, Albert gets (100/1000)x100=10 AP, as does Brenda (1000/10000)x100 and Chuck (10,000/100,000)x100.
Then let's say you've got (as per your FAQ example) 10 million DP to dish out, and a total of (say) 2,000 AP accrued across the site. Divide total DP by total AP, giving you a DP value for that month of 5000 per AP. So our friends above get 50,000 DP each (APxDP value), so $50 (which weirdly turns out to be the example amount in your FAQ). Someone who got 20,000 uniques for Skyrim would get 100,000 DP, someone who got 100 would get 500 DP, so it's still based on popularity, just now within the context of each game.
Does that make any sense? I'm sure there's a more elegant solution. It'd also need working on to avoid someone making a simple mod for a very, very obscure game, getting one download (maybe from a mate), getting 100AP and netting 500,000 DP. Maybe a minimum number of dls to be eligible and the game needs a certain number of mods in that month from unique modders? I'm sure a bit more maths could be applied to even that out. Some sort of taper like they use in benefit calculations. It's been a month since I've had a proper night's sleep, and three decades since I sat in a Maths lesson, so this might all be gibberish. Sorry if it is!