Although some hints could come from her showing up in D/P, proof that being there =/= getting hints is shown in a lot of AG when Misty is there, if anything, she seems to end up doing more with Max than with Ash. Though, then again, the other prior character appearance in D/P did leave quite a few hints for a different Ash ship and only a brief mention of the rivalship to it, so I guess it could go either way.
But yeah, if by rumours of Misty and Team Aqua you mean Misty being PART of Team Aqua, I don't think the idea of a friend of his joining a villainous team would go over too well with Ash. Would probably lead to more hints against Pokeshipping (and more for another one of my ships) than hints for. After all, it doesn't help that Ash comes to conclusions quickly, so even if it was only undercover or whatever, would probably take a hell of a lot of explaining to do, and Ash's patience, I'm sure you all know, is well-renowned (/sarcasm).