In the US there was the Sega Vs Accolade thing (
http://cse.stanford.edu/class/cs201/projec...engineering.htm ). Now even if that failed (and it is a key ruling forming the basis of the electrical/computing industry) it would probably fall under the reverse engineering for compatibility "exception" of the DMCA.
This however is US law and European law is somewhat different (I have little knowledge of German and French law in this matter but a lot of this is common to Europe by way of European directives and participants from all the countries agreeing to various things at conventions), broadly speaking in many ways it is better (not quite so many stupid laws) but it many ways it is worse (a lot of stuff is not very clearly defined).
However I will add this is why you occasionally get older GBA homebrew coming without a header (or a "proper" header).
As for the matter at hand assuming the logo is indeed copyrightable* (trademark sure but then the vetting process which amounts to little more than pay us some money has the potential to be questioned) then they may have a leg to stand on.
On the other hand it could be dubbed fair use and as no company to my knowledge charges for updates to the software/loaders... so profiteering by means of software with the use of a copyrighted work belonging to someone else may not be an option. Fair use is not a very well defined term in Europe when compared to the US (in the UK at least strictly speaking you are not allowed to copy a CD but it is almost never pursued and is really only there as a get out clause (I can not necessarily sue a company for loss of my fair use rights because of their actions)).
*copyright is the protection of a work (a piece of art, a film, a song, some lyrics), trademark is the protection of a brand and usually extends to similar brands, servicemark is like trademark but for services (I mention only as software as a service (SaaS) is the buzzword of the moment) and patent law would probably not apply here (not to mention it would likely have to be a software patent which is a almost non-existent concept in Europe).
The logo needs to be there too effectively making a protection method and because of this it potentially falls under cryptography law which tends to read "if it is there (and implemented "properly") it is illegal to circumvent however useless the method is". Such a method I would argue does not constitute protection as no real method of stopping the area being read is in place.
It also depends on whether the logo was obtained via dubious means. This would mean the nitroSDK, parts have been leaked over the course of things in which case it would probably be similar to the nintendo vs atari in the US (the link above has a note on it) and more recently the majority of the original xbox homebrew) or via legitimate reverse engineering (in which case the logic behind sega vs accolade comes back). To prove such a thing would be mightly difficult as well (if the logo is not there then it does not work so there is little chance of "errors" being matched which is the usual method of proving a work has been copied).
At the end of the day Nintendo has lawyers on the payroll and even the biggest retailers (the likes of divineo) would be put under serious financial strain to mount a decent defence which seems to be the main method by which legal manoeuvres such as this work.
Best route, as I recall the logo is only a CRC16 of a small ish file. CRC16 is fairly weak and I should imagine not especially hard to generate a collision* for.
http://nocash.emubase.de/gbatek.htm#dscartridgeheader
0C0h 9Ch Nintendo Logo (compressed bitmap, same as in GBA Headers)
15Ch 2 Nintendo Logo Checksum, CRC-16 of [0C0h-15Bh], fixed CF56h
*a hash takes all the file and makes a number sequence to represent it (kind of like odd or even), a collision is where two different files produce the same hash (which statistically speaking has to happen for a file longer than the resulting hash but for a good algorithm for making sure a file is unchanged is very rare and incredibly hard to do anything with).
http://www.cryptography.com/cnews/hash.html
edit: Densetsu3000 is right, it seems I did get a bit parenthesis happy. Post tweaked a bit.