As you rightfully noted, numerical note names have a couple of advantages compared to the traditional (western?) note names. Heck, the common thing even falls completely apart when dealing with any other than standard major or minor scales. And when transposing scale, the traditional names really complicate things (compared to e.g. variants of movable-do-solfege-syllables (am I using the correct term here? i'm rather unfamiliar with english terms in this area)). When working with other scales, in particular ones not even based on samitones, the names completely lose their relative meaning.
The traditional names, however, also have advantages: 1. it's by far the most common way to describe western music and thus, for most people, the easiest to work with. 2. for people with absolute hearing, the note names carry a VERY strong relation to the actual sound frequency. Also note that C# and Db are only the same frequency when using equal temperament. They may actually differ with any other temperament, in which case a simple note numbering system then falls apart - completely falls apart in fact.
Trackers historically have been tied very strongly to the standard western equal temperament 12 tone scale and tuning (12TET). This assumption is somewhat deeply embedded in the OpenMPT code base. OpenMPT already supports almost any other possible tuning and scale by using custom tunings (with varying ease of use depending on how much it differs from 12TET). So, when not working with the default 12TET scale, one can already (somewhat) freely assign note names (or numbers for that matter).
However, the pattern display code still assumes a 3 character note name. The drawing code for the standard bitmap font even has the actual default note names hard-wired. Thus, until someone takes the time and completely rewrites that code path in a more flexible way, we are very much limited to that format.
I guess, touching that stuff MAY be most useful when overhauling the whole custom tuning machinery (which is, albeit VERY low priority, already on our todo list).
Please do realize that OpenMPT is developed by only 2 developers right now in our spare time. The code base is really old and requires substential amounts of refactoring maintenance to keep up and working at all. The time that remains when these necessary things are dealt with, is generally spent on features we ourselves consider most useful and want to work on. A more flexible note name display has advantages for sure. It's just that there currently (and in the near foreseeable future) are (for us) more important things to work on.
However, I actually do think we can make the default names configurable at least within some strong limits right now: 1. Limited to 3 characters per note. 2. Not fully flexible when using the standard pattern font. 3). Only plain ASCII characters. That would be a rather simple change I think. I think I'll try that once I find time for it.