I would replace the brakes with something like the TRP Spyres, you will get a bigger pad and dual piston actuation. Those tiny BB5 pads and other similar tiny pads just don't give you much real estate to stop with. The TRP pads are also Shimano compatible and are used by probably 50+ different brakes (From Shimano and TRP/Tektro) so there is a really good chance of finding pads. not that BB5s are exceedingly rare but I see them a lot less then Shimano and Tektro.

More importantly I would replace the cables and housing. You want housing that is compressionless and you want a cable that is slick, smooth and stainless. I would recommend Jagwire's Elite Link kits which come with everything you need. I will say with disc brakes you may need some extra "beads" so you might especially if you have a hybrid or MTB with cable brakes is get yourself the mountain kit and buy some road cables and now you have an extra set of cables for those other bikes.

I would also get good rotors if you have 6 bolt the Shimano Deore XT SM-RT86 is a good choice and with good fresh pads from one of the Stops (Kool or Swiss) will help quite a bit. Larger rotors can also help but you will need the right adaptors for it assuming they can fit.

If you really want Hydro discs TRP HY/RD is you best option as it is cable actuated until the caliper where it switches to hydraulic braking so you don't have to swap levers and all of that which is expensive though honestly I the Spyres are just fine and dandy.