Absolutely! Sunshine Seasons, for one (LOTS of choices there, each station has different things). Electric Umbrella for two. The Cantina in Mexico did have outdoor, but *might* have indoor seating as well. Maybe. Didn't go there or pay much attention.
There's a bratwurst/pretzel/beer place in Germany, looking at the map it might be called Sommerfest, and the seating seems to be indoors, but during the cold snap while we were there it was FREEZING. So it might not be immune to the elements. Tangeirine Cafe in Morocco has indoor seating, but not much. I would go at "off" times for that one.
There might be others. I googled "epcot map" (b/c I can't find the maps I've been using to help with my trip report) and found the wdwinfo.com one, and the ones NOT marked with "R" are counter service, and then I went through the ones that I actually noticed or went to.
It seems that the American showcase restaurants are CS, but I'm not 100%, and I have NO idea if they have indoor seating. But I'm sure others can fill in the blanks!
Sunshine Seasons, seriously! In the same building as Soarin' and Living with the Land (and a couple other little things). Park the stroller outside, though!