Music notation is a mess.
I'm not proposing changing it (that would make no sense -- it's good enough), but it's not worth treating as somehow right. Centuries of unplanned historical evolution don't necessarily result in something rational.
To go with your analogy: it's like the legacy software system written in Fortran which runs on VMS. There's a ton of institutional knowledge and good ideas, but a ton of cruft too.
In that sense it's much more forgiving than software. Software becomes indecipherable almost as soon as nobody is looking at it and its structures are in some sense necessary for a purpose. It's not as amenable to pragmatic solutions although often, more of them are possible than we recognize.
A lot of the notation of timing is cumbersome. Why the large number of wonky-looking symbols? Compare to how a lot of composition software shows timing with how long a position notes take up horizontally (music notation predates the concept of Cartesian coordinates!). It's a lot easier to work with, in all respects.
All this stuff builds up to about an unnecessary 3-month learning curve for kids learning music notation.
Is it worth changing a whole industry -- where everyone already knows the notation and there are countless works in notation -- to save all kids three months? Maybe, but probably not. That's the legacy system problem.
The nice thing -- compared to software systems -- is that none of this stuff is really all that complex.