A low bearing count, in and of itself, is never better than a high bearing count. However, a high bearing count does not necessarily equate to a better reel. Case in point: The Shimano Citica E VS the Shimano Caenan, which has more bearings but a graphite frame. Those extra bearings won't stop the graphite reel from flexing under load. I'd take a Citica over a Caenan any day of the week and twice on sundays.
I wouldn't mind seeing more reels like the Citica E, which is built with close tolerances but with only three ball bearings. If you want more bearings, you can add them yourself, but the stock Citica is a sturdy and smooth platform.
Now, someone mentioned three spool bearings as being unnecessary. I used to be of the same opinion, but now I'm not so sure. On reels like the Citica and Curado with only two spool bearings, there's more potential for the spool shaft to bend. When the reel is in gear it's fine, but put too much load on the spool when the pinion gear is disengaged and the shaft can bend. Just the other day I was handed a Citica D to clean, and that particular reel has a warped spool shaft from too much pressure being exerted on it. Obviously this is not a common problem, and I'd guess that it happened while the clutch was disengaged rather than while fighting a fish.
On reels such as the BPS Extreme or Pflueger President baitcaster, the three spool bearings are located as follows: One in the palm-side cover, one set between the spool and the frame on the handle-side, and a third bearing under the spool-tension knob. One of those bearings isn't really necessary, but not the one you might think: The bearing under the spool-tension knob. Look closely at the spool shaft on such reels, and you'll see that it does not fit snugly inside the bearing. This is intentional. When the spool shaft flexes very slightly under load, that bearing comes into action and helps keep the reel running smoothly. A bushing would probably serve instead, but it would have to be a metal bushing rather than nylon.
That third bearing has no effect on casting, so it doesn't really need to be upgraded if you want to increase casting performance.
Whether a three-spool-bearing design is more or less effective than a two-spool-bearing system is up for debate, but I'd be inclined to say that they're just different, and neither one is really "better" than the other.