I've R&R transmissions off and on now for nearly 6 years I guese and have yet to see a transmission without a filter of some sort. I've only ever seen one that I can recall that didn't require dropping the pan to replace it, and it was on a front wheel drive.
The majoraty of the filters are throw away. If you wanna find out if they did drop the pan they should have cleaned it while it was down. If you take it back and they say they did drop it I think I would ask them to drop it again if the gasket doesn't look new ( note here some gaskets are reusable if it's a cork gasket it is not) . If it wasn't removed and you " do not have any minor problems or major problems" witht he tranny the pan should still be fairly clean. If it is cleaned then you may be responsible for a gasket, fluid, and labor.
By fairly clean I mean you may find some clutch dust even if it was done properly and posibly some metal or brass shavings this is normal. You can't hardly flush all of this stuff out it sticks in the cooler and converter and so on and will show up in the pan often time on a fresh rebuilt unit too from the cooler or lines. If the pan has a magnet in it like most any self respecting mechanic would clean it. You will deffinatly know if it wasn't cleaned as it will have like a 1/16" or more of goo on it.
For the record I have never had the pleasure of pulling a tacoma or even an older toyota automatic. So I can't say for sure the gasket type or filter type, but I'm sure someone will chime in with this info. The above info is an observation from the some odd hundred I've pulled.
There is also a website called http://www.atra-gears.com
that lists shops. They stay pretty on top of there list I think as they also supply technical info to rebuilders. Ypu might want to look up the shop you went too.