I have managed to sort my save game now, turns out I forgot my ship was a modified Griff Cobra Mark III as I replaced the decals on mine and customized the colours a bit. The only missing equipment now are OXP equipment without the "available_to_all" = 1;
In the past only on buying the check was made if a ship was allowed certain equipment. Even the repair of not-allowed equipment at the normal outfitting screen, was possible. (I just tested it out with 1.76) That could mean that when you changed your player ship by editing the save file, any not allowed equipment for the new ship was not removed and could even be repaired. This editing of the saved game could have happened 'ages' ago.
I'm glad it is sorted out now and was not a bug in Oolite itself.