Proper way of choosing hubs
If you are having to service hubs after a 50km ride in wet and muddy conditions something is wrong. All bearings on modern hubs are 'sealed'; not hermetically, but enough to prevent ingress of water and dirt and should not need servicing so often.

Just to address you other questions:

Re 'industrial bearings' I think you mean cartridge bearing types (which use industrial standards for sizes and quality). You don't need these per se. Cup and cone bearings work fine.

You cannot use through-axles on a frame designed for quick release axles. Some hubs are convertible from TA to QR though.

Center lock and 6-bolt rotors are not interchangeable.

With inexpensive wheels it's not cost effective to replace hubs because new hub, new spokes and the cost of rebuilding the wheel is comparable to the cost of a whole wheel.