It is usually easier with a GBA slot device but are there not wifi dumping tools that also do saves?
You will also need a copy of netcat for windows which should be easy enough to find.
I am not sure about Rudolph's wifi stuff (got GBA slot devices when it matters there) but it looks like it does wifi over FTP if you prefer that to netcat..
i think there are ROM dumpers that can also do hotswapped save insertion? but the slot2 version was the one i use before (inserted a save file into retail Strange Journey, because my playthrough on that is insanely long).
I think it's the NDS Backup Tool. not sure which of the three (there's 3in1, Slot2, and Wifi versions), but i think all of them can copy/insert saves from/to retail carts. the first two need to be run from slot 2 though, and the third requires an FTP server running off of a computer with wifi connection.
There were a couple that attempted DS slot hotswap but most DS carts do not initialise the memory card or much of anything after a hotswap so that technique was largely abandoned in favour of DLDI GBA slot stuff, hotswapping the 3 in 1 or wifi via FTP or raw transmission the likes of which people use netcap as a simple way to handle.
Rudolph's tools which you mention (they went by the name NDS backup tool) did have save support where the later wood dumper did not which has led to some confusion.
Further back in time there were also programs that allowed you to dump to the SRAM of a GBA cart but let us not go there.