Curious, where were the Hoenn & Kanto "hints"? You could consider the references they made as hints, because I don't remember seeing anything about Hoenn/Kanto. But even if so Kanto could be in the remake thus adding to the "hints".
There are some references to these places, although if I remember correctly, some were only in Platinum.
However, I'd add that in my opinion, they were less noticeable, and plentiful than the numerous references Johto had in D/P/Pt. It was basically a goldmine, really. One can say 'so because they mentioned Hoenn, it means they're making a RSE remake this gen too', which is obviously not true, but fact is, these references are fewer in number compared to the references to Johto and events in GSC - far more specific as well, I might add.
Rather than just general mentions of the region name (e.g. 'I was born in Hoenn!' 'I want to go to Hoenn for my vacation!' which makes up a number of those references listed in that link posted above (and some are vague - foreign dex entries being the same as FR/LG, and choice of Pokemon in PBR seemingly so), they went to Johto-specific events constantly - Red Gyarados, Eggs, Prof. Elm, Whirl Islands, Ragecandybars, a 'Dragon-taming champion' (Lance)... One mention to Kanto also doubled as a reference to GSC - mentions of Clefairys dancing at Mt Moon is one, as the Clefairy dance only occured in GSC. They also play more of a part in the game, making them more noticeable (Red Gyarados show in the intro of DP, the SecretPotion a necessary Key Item, etc, etc), as opposed to people just saying 'I came from here blah blah blah').
Such a number of references were hardly necessary (heck - why would they have Jasmine give you Waterfall when anyone else could have done it, for instance?), so I say it's fair for some people to take it as hints, really.
Not that references meant they were making it then already (this was an argument made many a time before the games were announced), but it does show they considered it, if you also took note of the in-game coding, allowing Pokemon to say in their status screen that they came from Johto, even though this is impossible until the release of the GS remakes here. (And the fact Jasmine had a sprite already).
Apparently, according to articles they've been working on this game for at least its 3rd year now, so one can't say they were really already working on the during DP's release, but they certainly had considered it, and already had taken measures then for it, during its development.