I found the japanese subtitles for the k-on movie on kitsunekko but the format is .sup, vlc doesn't play them and aegisub doesn't open them. I read on google that this format comes from blu-ray movies but I couldn't find anything on how to get them to work. I don't really know much about this stuff, so I was hoping that somebody here could help me out. Since this kind of subtitles seems to be image-based is there a software to add them to the mkv file in order to get a hard-subbed output? I'd rather keep the subs and the video separated but anything will do.

Yeah, .SUP files are Blu-ray imagesubs. Just like DVD VobSubs, they're in a binary format (i.e. not text-based like .SRT and .ASS [etc.] subs), so you need to either OCR or transcribe them so that you have them in a textual format. You can use Subtitle Edit, but be warned that the available free/open-source Japanese OCR engines that work with Subtitle Edit lead to a lot of OCR errors in my experience, so transcription is IMHO the only real option.

Also, you can simply use mkvmerge gui (mmg for short) and mux in the .SUP files and they should play using MPC-HC (e.g. using the Kawaii Codec Pack, CCCP, or the K-Lite Codec Pack). But you'll still need to do transcription/OCR if you want subs that you can use with subs2srs. Alternatively, you could use a program to convert the .sup file to the VobSub imagesub format, which is at least more widely supported at the moment than Blu-ray imagesubs are.

Thank you Morellet I'll try using mmg, since I don't really care for subs2srs