Yes, analog EQs do degrade the sound (many digitals do too).
You can get analog mastering EQs that cost a fortune and do less harm, but Yamaha never made any - not for consumer or pro market. They did/do make EQs, but not in this quality.
Some setups do have large issues where a "normal" EQ can help, but this is due to the problems being so big that the EQ "thing" disappears in bigger problems. The best fix will always be to fix the room and setup, rather than applying an EQ (EQ is the last resort).
In the audio recording world there is a saying that if an instrument sound wrong, you do not start applying an EQ - you change the microphone.
HiFiCanada; if manny CDs have too much bass, then it is not the CDs but your setup that needs to be looked at - Check for room notes and so on.
Yamahalic; get rid of that EQ
Remember that mastering is a mix of technical skills and artistic decisions, it might be that you do not like the art and will be better of with a different version. That said, there are many early digital re-mastering editions that suffers from too much treble, but acting as you're own mastering engineer is seldom the best solution. I work with sound for a living and when I play around with an EQ in my Hi-Fi setup I usually come to the conclusion that I made it sound different - but not better.
The number one key to good sound is the room, and you can't EQ a room.