GBA slot unlocks usually have two forms
1) basic presence detector
2) save loading/fiddling
2) is far less common, though it does include pokemon so a lot of people are familiar with that. Megaman I believe has examples of both types.
1) is split into two further subtypes. The first is just having there are one point (maybe at game start, maybe at some other point) will allow you to unlock some bonuses and you can ignore it. The second needs to be there all the time.
On 2) the trouble usually is GBA flash carts use SRAM where most games will tend to be EEPROM of Flash and the DS rom itself is coded.
To the best of my knowledge you can not use the DStwo to emulate a cart as it were, you could use cheats like you can use with any other cart, you can use a 3 in 1 or something like you can use with any other cart and you can grab the save and use it with desmume.
http://www.gamefaqs.com/ds/928331-mega-man-battle-network-5-double-team/cheats lists them for MM5 for the DS. Do a page search for "slot" and it covers all of them.
Though I said cheats I am not aware of any offhand that will work to make the game think it has a GBA cart inserted, you might be able to fake the items/points/sounds though with more normal cheats.
Likewise I am not sure anybody has made a patch the pokepatch to allow the DS game to read from SRAM to use with a 3 in 1.
If you are up for making some cheats to do it I am up for helping out, I imagine it will be done in one of two ways.
1) You fake a return from the GBA slot read, it will probably only be a header read as reading the whole thing is pointless. You fiddle with this read/return.
2) The game sets a flag somewhere in memory after the header read. You edit this memory value instead.
Editing the GBA to read GBA saves will be more tricky. That said MM5 on the GBA uses SRAM so you might get lucky.
