For the missing tracks in Ys, it's probably a
space issue.
Even though the media was considered incredibly huge back at the day, CDDA ate up a VERY large portion of the disc, and that in the original Red Book specification, a disc could only hold up to 74 minutes of audio, and according to Yellow Book, only up to 60 minutes(or, around 540MB) of data. Also, disc mastering wasn't reliable at the time, when a disc hit the 70-minute line and Ys was already close to the limit. Nowadays CD-R(OM)s could reliably hold 700MB+ of data, but it's not the case at the time.
The development team had worked very hard in calculating space usage, especially in the audio apartment, that each music track should be either CDDA, chip tune, ADPCM(and there were cut-scene tracks), how long each track should be, and some of the tracks had to be outright omitted. Even the boss theme of Ys II had to be dropped, which they regretted, that if they could put 2 more minutes into the disc they wouldn't make this omission.