Yes, the insinuation that Trump and Putin are having an affair does have slight homophobic undertones. But a couple of things should be kept in mind:
- Trump and his followers are incredibly bigoted, so insinuating that "their guy" is engaging in the type of activity they oppose is the point. (In a way, its like the neo-nazi who believed in the 'one drop' theory of racial purity finding out that he actually had some genetic heritage from Africa.) Its not the 'Trump is being gay' that is the main part, it is the 'Trump is engaging in activities that he and his followers condemn'.
- The type of 'relationship' that they are accused of is not strictly a 'homosexual' one (with both individuals on relatively equal footing), but one of master/slave. Trump is obviously subservient to Putin. The same sort of criticism would fit if it were Ivanka Trump who was elected thanks to the support of Putin, in which case suggesting she were also submitting to Putin would also fit
You're right... its not very imaginative. But, not every joke/criticism has to be uber-witty to be funny or effective. After all, Trump got elected even though the greatest height of his imagination seems to be coming up with childish nick names for his opponents.