Notes, keys, and questions.

For instance. "My system handles B-Major much better than D-Minor."

Do you know how hard it is to come up with something that gets ZERO Goolag hits? That is some "for instance"! No one ever, ever said anything even remotely like this. 

For the very simple reason that what key the music is in is of a completely different order than what instrument is playing the music, regardless of key. It is the challenges of as frogman said, faithfully reproducing the sounds of the individual instruments in all their timbral and dynamic complexity that our systems do poor or well. If your system faithfully sounds like a real live guitar then it will faithfully sound like a real live guitar regardless of what key is being played. 

And yes, I grew up being taught to play piano and accordion in grade school, and played french horn all through jr high and high school. Along the way learned to play trumpet, and even a little sax. Later on learned harmonica. The main benefit being what frogman said, a lot of first hand experience with the way real musical instruments really sound. He describes it very well indeed. 

I'm a guy who plays several instruments and isn't afraid to play each of them in a variety of keys.  That said, apart from strange room resonances or something rattling around in the room or inside the speaker, it shouldn't make one iota of difference what key a particular  piece of music is being played in when it comes to hi-fi reproduction.

I'm at best an amateur.  But I would often test this on my mother:  "Hey ma, play me the slow movement from Beethoven's sonata-whatever."  She would.  I'd then ask her to transpose it:  to Ab, to C#, to the most remote key I could think of.  She would, and ALWAYS would say "See?  It's all wrong!" even though I could hear no difference other than pitch.  Now she was playing a modern piano, tempered so that the only difference between the relation among notes was pitch.  But to her ear, each key had a specific 'personality' and that was that!   The only explanation I have come up with is that she associated certain keys (I'm assuming she had perfect pitch or close to it) with other orchestral or chamber pieces in that key involving  instruments where key selection is important (getting on the fringes of my competence here, but you wouldn't ask a folk guitarist, say, to fire up a song in F#); she thus 'heard' each key within the context of the entire classical and jazz repertoire in that key.

By coincidence, I was writing a post in another thread about the idea that putting as much (or simply more) effort into learning the language of music as is often done learning the technical language of audio would result in more
common ground in discussions among audiophiles; and more civility as a result which was the thrust of that thread.

While the idea that a system can handle one key better than another is a new one to me, the answer to your question is yes, I do “translate what I hear into defined notes and keys”. Not always as a conscious or deliberate effort, but usually as at least the backdrop to the experience. That may be the source of some confusion around your comment about systems and keys. What I mean is that all keys have certain “personalities” or “flavors” beyond simply being lower or higher. Composers choose to compose in specific keys for that very reason. A musician becomes sensitive to and learns to identify the differences in the “personality” of certain keys. I don’t believe that it is the case that certain audio systems do better with one key or another.

More importantly, IMO, as concerns audio, is the fact that not nearly enough attention is paid in audio forums on dynamic nuance and texture in the timbre (tone) of instruments as a means to describe what is heard. Musicians are obviously around the sound of live music a great deal. Several hours a day in the case of a working musician. Live music contains a tremendous amount of detail in the two mentioned areas (there are others); far more than even the best audio system can reproduce. This is greatly responsible for the emotional response to music that a listener experiences. Subtle dynamic nuance is what mostly determines the music’s feeling. It affects a listener’s perception of, for instance, a singer’s phrasing and the groove (or lack of) in a drummer’s playing, among other things. Inner texture in the timbre of instruments is also another aspect that often gets short shrift. The result is confusion and lack of common ground in the use of terms like “accurate”, “bright”, “clear”, etc.

Unfortunately, the idea that the aspects of sound that are discussed on forums such as this should be related to the sound of live music meets with a lot of resistance in audio discussions. It would help a great deal if that was not the case.

Having said all that, it’s important to understand that musicians don’t always analyze music this way when listening for the simple pleasure of listening, but these are things that inform our reaction to music. 

And all this is just scratching the surface. Good question.