I used the adapter variant. Bought the parts from infinitydream.com, which is a french console modding shop. They did the soldering of the USB port and the USB cable, i just had to solder the loose wires of the USB port to my 3DS XL´s board. Luckily my father has a "normal" 35 in 1 card reader, and that one works. Seems like those card readers which are constructed as a stick don´t work for me. I dont know why. But that working card reader of my father also produces the same size of NAND dumps with stable md5 hashes.
I will try and get one of those on tuesday.
EDIT: Just revived my old WinXP netbook, ant its internal cardreader also gives me a dive. I have a working solution for my dumping needs now
EDIT2: Just jumped into the cold water now. Quadruple-checked my dumps made from various cardreaders and my Gateway 3DS, all share the same size and all dumps from one source share a single md5 checksum. Updated my sysNAND to 7.2, downloaded patches for Pokemon X/Y and Mario Kart 7, made some adjustments in my system settings and dumped my 7.2 sysNAND. Reflashed 4.4, and it works flawless. Now i search for that little program which allows me to inject my dumped sysNAND into the emuNAND partition.