There is no reason for this to be DSiWare. First off TWL mode would not have as much resources for the GB emulator that this title will have so performance would not be as optimal. (though it's GameBoy we're talking about here, I don't think it would have made much of a difference).
And second it's advertised as a 3DS game. NOT a DSi Game!
The Legend of Zelda: Four Swords Anniversary Edition was available on the DSi and subsequently available on the 3DS as well since the 3DS included all previous DSiWare on the eShop as well. Can you still obtain that Zelda game from DSi eShop on a DSi? I would think so unless it was a special limited time run.
Point is, VC games run in CTR mode which means all the available hardware like Wifi and stuff have been available for them to use this whole time. The only reason we haven't seen any VC titles make use of the new hardware is because Nintendo simply chose not to put in the work to add that support. Some changes to the game roms may be needed to do that.
Nintendo has for the most part just doing quick VC builds with unaltered roms to fill their VC catalog. So for the sake of quantity, they probably didn't put a whole lot of work into them. Hence why we haven't seen anything fancy like online play for games that used to use link cables. It would require changes to the game roms and a reworking of the VC environment they setup for it to make it happen. This would add to dev time and increase costs. So they chose not to do this.
But with Pokemon being a pretty large game franchise and trading/online play an important aspect of it, they decided to go through the extra effort to enhance the VC emulator they are using to run this game. The pokemon games all sell well so unlike the shovel ware VC games they push out they expect to get a lot of sales for this and thus justifies the extra time and effort into improving the rom and VC environment.
It's highly unlikely this will be running in TWL mode. It makes no sense and anyone familiar with this system and how Nintendo has made and marketed games for it would know that.
That said, don't expect to be able to just inject any game rom you want into this and have the online stuff work. The game roms being used have likely been modified and tailored to work with the new features they added in the Virtual Console emulator they are using for these specific games. Because it uses online play, there is a good chance they might have removed the old MissingNo glitches and Mew glitches. Unless they decided to add legality checks on their servers like with gen 6 pokemon games. Though even so, they'd fix these glitches anyway. They are widely known and since they are already having to modify the roms to make online stuff working, patching out the glitches would be easy for them. I say there's a very high chance the MissingNo/Mew glitches will be dead and buried in these new VC games. Nintendo and Gamefreak have been pretty airtight on trying to get rid of glitches and bugs that might give players an unfair advantage. Just look at all the game patches they've introduced for the gen 6 games. The 1.3 patch for X/Y being a notable example where they blocked hackmons from being used in passer by battles.
Hell there's a chance they may have completely rebuilt these old games and there isn't an emulator running this at all! There may be no rom to inject! Much in the same way that the Zelda game people keep bringing up, they may just ported the game assets over and rebuilt it. The games were pretty simple compared to today's games so it would probably be pretty easy to do if they wanted to.
Although some with the ability to repack CIAs and run them on exploitable consoles might be able to bring the old glitches back if someone figures out how to undo the fixes to the rom while keeping the changes that made online play work. That's not out of the realm of possibility if there's enough people who really want to do those old glitches for some reason.
It would be cool if Pokebank could allow transferring pokemon caught in these games into our gen 6 games. The old gen 2 barrier would finally fall away. But that's unlikely. I don't see it happening.