No, the servers are not down
I've tested several games the last 24 hours and all the games I tested worked, except for Custom Robo Arena. I believe there's a problem with my setup/ backup or whatever... I've been using my DSi with acekard 2i to connect to Desmume.
Anyways, I believe the online store not working on Fire Emblem might be because it requires an additional server, much like the ones needed for Pokemon, that are more or less fixed thanks to a different comunity. I haven't tried it, so I can't say for sure. There's no entry for it on the compatibility page over at github, so I guess I could test it for you, but only if WFC don't come like 5 hours into the game... In that case I'd have to kindly ask for your save.
Furthermore, I recommend people interested in playing online to scroll down to the bottom of the github page where you can find the link to the altwfc comunity chat and as always read the guidelines for the chat:
https://github.com/polaris-/dwc_network_server_emulator/wiki
There's even a cool stat feature that let's you see if someone's playing and what they're playing.
Bunch of applause to the people who made this, since it's usually very stable (I've played through FFCC:EoT without problems) and not to mention awesome! You can even make your own server from what I can gather...