In the early seasons his homosexuality seems to be there for no reason other than to make jokes. There was even a scene where he was at the hospital and it's insinuated that he has a foreign object stuck in a certain body cavity.
Do you consider these depictions to be homophobic?
Well, I guess there is a limit to what the Simpsons could get away with. The Simpsons has always been a progressive show and did feature gay acceptance episodes but yeah, the earlier depictions of Smithers may have been a bit crude. That's the depiction of homosexuality that the era allowed.
The early depictions of Smithers wasn't even supposed to be gay at all, it was only in later seasons when the writers ran out of ideas that they made him gay.
Originally, Smithers was just a parody of the stereotypical 'toady' who is slavishly devoted to his boss. and Smithers wasn't gay, he was in love with everything Mr. Burns said and did, he was, as Matt Groening has said, a 'Burnsasexual', but he wasn't gay.
The only thing that the early seasons were implying was that Smithers, who even dresses boring, has a really interesting life outside of work, and we're seeing little weird snippets of it. Like how he speaks Swahili, and wrote a musical about Malibu Stacy. I don't feel like his being gay and his being significantly less boring outside of work necessarily go hand in hand.
______________________________________________ Formerly known as "Greenmandms"
The DVD commentary for the "Tell Tale Head" (which was the first episode to imply that Smithers had feelings for his boss) does imply that the plan was to make Smithers gay from the beginning. I haven't listened to it in years, but I'm pretty sure they say something along the lines of, "Sam Simon suggested early on, let's make Smithers gay."
At any rate, the whole "Burnsexual" thing was definitely out the window by Season 7, where there are ton of coded references to suggest that Smithers identifies with the gay community in a much more general sense ("I tried to march in that St. Patrick's Day parade," "I am partial to Jolly Ranchers"). Not to mention, he goes to a gay nightclub while on vacation.
To answer the OP's question, I can see why some might find the "wink wink, nudge nudge" manner in which Smithers' sexuality is subtly implied to be a bit homophobic by today's standards, but then the 1990s was very different age, and mainstream television in general tended to be a lot more iffy on the subject.
Did the forgotten generations scream or go full of resignation, quietly protesting innocence?