Sesame Workshop has made their stance clear. (repeatedly). I don't know about the T-shirts and merchandising- I'm not sure if all of those are actually licensed by Sesame Street in any case. If so, then as others have said, it's probably Sesame Workshop giving the sly wink...
But yes- people are going to interpret Ernie and Bert's relationship as they choose to, regardless of what the official statement might be.
Of course, considering the age range of most viewers of the show (at least the ones that it's aimed at), I really don't think any sexuality is appropriate at that age level. (At least not into the specifics of course. I realize we've already had Gordon and Susan adopting Miles and Maria and Luis getting married and then Maria giving birth to Gabi- but obviously on a simplified level.) If we're educating kids for kindergarten and elementary school, let's stick with numbers and letters and save the sex ed. class for middle school.