I don't think there are any dedicated tools for GBA Harvest Moon titles, indeed there are surprisingly few dedicated editors for GBA games. You might find a few documents or posts detailing it for while not so many went in for the GBA Harvest Moons (between bugs and mechanics they are not exactly exemplary examples of the gameplay style) you are far from the first to want to look at it.
It should also be noted that compression was not new on the GBA but newly available to be used all the time if devs wanted, and they often did (or at least cartridge size mandates demanded they did).
I cover a few GBA capable tile editors in http://www.romhacking.net/forum/index.php?topic=14708
but it is mostly tiled2002 and crystaltile2 for the basic stuff that people playing GBA hacker tend to opt for when needing an editor, with a few others for viewer or compression aware viewer (crystaltile2 has some limited abilities here as well, personally I tend to figure out the compression by whatever means and go manual with another tool before feeding that back into CT2 or tiled2002).