Your point about emissions I think is probably an important one why manufacturers don't spec manuals anymore.
First the take rate is pretty small these days
But this is not what I'm finding looking for Tacomas. They offer a 6 speed MT on all the models and finding them is tough. Dealers can't keep them in stock, they go from Craigslist fast. Same is true of the Nissan mid sized. One dealer told me he can't seem to pry stick shift Tacomas from people on trade-in, they do better selling them on Craigslist than anything he can offer. Maybe it's a regional thing, Toyota mini trucks in general have cult status and command a premium in Colorado.
Our search is for an Access Cab (their extended cab, not 4 door crew cab), V6, MT, TRD with under 30K miles and we might find one comes up every week or two in Internet searches. We call the lister or dealer and it's gone already. You have to be ready to go the day it lists it seems. We'd even consider brand new but we'd at least like to test drive one and no one has 'em. The 4 door with short bed and autos, every dealer has half a dozen of those used on the lot.