Probably a stupid quesiton... but what's the point of a 64bits Winbox ? what use case / config would require it ?
Even though the name of tool is
winbox which implies it's a tool running in windows (and that's even true) that doesn't mean it can't be run in other environments. Such as under wine in MacOS (wine is windows emulator for other OSes, started off in Linux). And recent releases of MacOS removed support for 32-bit executables, which proved as final push for MT to deliver 64-bit versions of winbox (previously they tended to see matters in similar way as you do). As @rextended wrote it's just a matter of time when some other major OS vendor removes support for 32-bit executables from their OS.
When talking about 32-bit versus 64-bit it's not only "bitness", it's also set of other CPU capabilities. While 32-bit executables are supposed to run also on historic CPUs (like 80386), 64-bit executables can expect to have much more modern CPU, supporting some useful extensions (such as SSE and other vector-like instructions) which help with much better performance. Surely 32-bit executables can make use of those features, but have to include legacy code (which is executed on CPUs without those modern instructions) which makes executables larger and harder to debug. One may argue that winbox doesn't need such advanced stuff and that's probably correct. But we're talking about supporting legacy systems here and if use of legacy systems is low it doesn't justify effort to support them.