Remember how the weapons/misc sprite editor contains a Boss Marker Misc Sprite? Well, as far as I know, the Boss Marker sprite doesn't seem to appear in Zelda Classic at all. Is it even implemented yet? Because if not, it would be a good idea to label it <unused>.
The Boss Marker Sprite
Currently, you are correct in that it's not used.
After spending 12 seconds thinking about it, a possible implementation might be something like:
0. It would have nothing to do with rooms marked with "Boss Room" flags
1. It would have a DMap setting, a la the compass and continue points
2. It would also have a DMap flag which would enable the use of the boss room marker (in combination with the compass), that defaults to off.
None of this is official, however, and I doubt I would get around to it, anyway...
As of right now, the misc sprite is named "MISC: <unused>" in the default template. Feel free to personally rename it in your quests.