Is there any way to use mini disks with vertical CD drives,
preferrably
an adapter when an external drive can't be used?
Ask the OP. Only he knows if he has or ever will have a need for
mini-disks. He didn't mention a need for a flash card reader, too, or
that he intends on using huge tower coolers on the CPU that would
break the tangs on the CPU socket if he went toting it around. If he
is planning for some future that may or may not pass regarding
equipment or media that he may or may not use then he will have
problems with the desktop case when, as yet another possible usage, he
later gets a different desk or lays out his gear differently and ends
up turning that desktop case on its side to then be a tower.
The suggestion of turning the tower on its side was if the OP truly
cannot manage to find suitable desktop cases as he claimed. No matter
which configuration you choose, it will have limitations for possible
future features. Since the OP seems to be squeezing the case into a
particular recess in his desk, dimensions will be the overriding and
critical factor in choosing a case whether for a desktop or tower
unit.
It was a pretty vague and generic question so I didn't bother going
into all the possibilities in limitations in either orientation.