With respect to Anime/Manga:
Again, here we see Pokemon-Human interaction far more than Pokemon-Pokemon interactions. And of the few Pokemon-Pokemon interactions very few of those are romantic/sexual in nature. Again, because of target audience, and for not having anything to do with the story line. Most of them involve adventures of protagonists fighting against antagonists, so there is more Adventure and a good-vs-bad vibe than there is a lovey-dovey vibe. Of course, this exists, but mostly as a filler and for the occasional fan-servicing (the SFW kind, to promote emotional attachment to characters to maintain a strong viewer base). Thus, the requirement for gay characters, whether we are talking Pokemon or humans, is slim to none, so we don;t see any of that.
Finally, it is hard enough to identify genders of Pokemon on-screen, so it's not easy to say "this is gay, and this is straight", simply because for most Pokemon, you can't tell the difference. In case you're looking for a conspiracy against gay propaganda (lol), then you can point fingers at broadcasting companies who will try to censor gay stuff. Off late, however, this is also on a decline, and there's not much you can censor from an animated show meant for kids (Not like Archer, for example.)
That covers what I think is relevant to Anime/Manga
Is the Pokemon Company homophobic? Is GameFreak homophobic? Is Nintendo homophobic? Is Cartoon Network homophobic?
No, of course not, they're corporations, you silly, they don't have feelings.
They have one idea and one idea only: Make more money. Generally, the whole gay spectrum was hush-hush because it was a taboo subject, and also because homosexual people were (and are) in the minority. There was no reason to affiliate with or against taboo topics because it might scare customers off. Not good for a corporation. However, nowadays, homosexuality has become more prominent and accepted, so it's not as much of a hazard now. It still doesn't mean they have to portray homosexuality. If at all doing that will bring them more money, trust, they will be the first ones to go for it. The day it becomes clear having gay Pokemon is profitable, the companies will over-saturate it to gain the maximum profit. They don't care about gay people; they don't care about straight people. They only care about money, and who can bring it in for them. That's not wrong or homophobic, that's just business. Nothing personal.
Another thing: A point to consider is that maybe having a gay Pokemon specifically, is, in and itself, a homophobic idea. Then, of course, any flaws we see in Pokemon becomes due to its choice of mating partner over other obvious reasons like stats/movepool/typing/etc.
Also, having a specifically gay Pokemon goes against the notion that certain Pokemon are different. By analogy, it can be interpreted that certain people are also different. And of course, every person is different, but I mean it in the way that gay people (Pokemon) are gay because of so and so, alienating them in the process purposely or not. The whole point of it is, gay people and straight people are the same in every (most) aspect(s), with one exception: Who it is that sleeps in the bed with them.
So, for all practical purposes, gay Pokemon exist; they are not shown for the same reason straight Pokemon are not shown:
- in the game, it doesn't matter, and makes coding difficult
- in the anime/manga, we don't see a lot of activity between Pokemon mating habits straight or otherwise.
We do have certain instances, like a male Kirlia/Gardevoir/Lopunny as well as Jynx and Mr.Mime, and those already draw a bunch of controversies. Companies don't like controversies if it means parents will stop their kids from watching/playing with the content they have created/broadcast.
Also, this was my interpretation of why/not homosexuality is shown openly. I might be wrong. Also, I might have made some statements that seem rude. That was not my intention. I don't have any sort of discrimination towards anyone. If you're still offended, I'm sorry, that is neither my intention, nor my problem, so I won't change any statements that are not factually inaccurate.