Why (if you had the choice) would you stay with cantilever brakes and forgo the opportunity to change to a disc set up for racing cyclo cross?
One good reason to stick with cantilever is easier wheel swaps. Last weekend races, my son flatted and we did not put spare wheels in the pits. Neutral support had spare wheels and if my son had a disc based bike he would not of been able to use them. Even if neutral support had disc wheels, with differences in rotor size they may not work for your bike.
Full Disclosure: my next CX will be disc based, I've been through too many rims with brake surface getting dished from grit and grime.
Professional cyclo-cross racers choose depending on the type of cross they are riding. On fast tracks or tracks with a lot of climbs they prefer cantilevers. On muddy tracks you see a lot of disk brakes.
I remember there was a huge discussion about this when they first showed up in the world cup (November 2013). Below some quotes from the leading riders in the UCI ranking at that time on the choice between disk brakes (hydraulic system) and cantilevers.
Lars van der Haar (current Dutch national champion)
"Schijfremmen blijven in alle omstandigheden praktisch even goed remmen, terwijl dat bij cantilevers in slechte omstandigheden toch vermindert." (Translation: Disk brakes keep working in all circumstances while cantilevers lose performance in bad conditions).
Niels Albert (Two time world champion)
"Met schijfremmen kun je kort voor de bocht snel afremmen, terwijl je met de klassieke cantilever-remmen al eerder moet beginnen remmen." (Translation: with disk brakes you can brake right before the corners, while with cantilevers you need a larger stopping distance).
Verstraeten, coach of Sven Nys (Two time world champion, current Belgian national champion)
"Mijn persoonlijk gevoel is dat schijfremmen ook een voordeel kunnen bieden in de modder. Met remblokjes wordt de remkracht toch beïnvloed door het vuil, bij schijfremmen niet. Maar het hele systeem weegt toch een halve kilogram extra. Het wordt dus afwegen." (Translation: I personally feel that disk brakes have an advantage in mud. With cantilevers the braking power is influenced by dirt. The disk brake system is about 0.500 kg heavier, so you have to make a check-balance).
On the highest level, the extra weight of the disk brakes will have impact on the performance of the athletes. I think however that on a recreational level, when there is still a lot of improvement possible on your own weight, overall fitness, .. I would go for disk brakes if cost is not an issue.
The superior modulation that most disc systems have is due to the hydraulic actuation not the fact that they are discs. Traditional Bowden cables have a lot of inherent friction. Hydraulic rim brakes such as the Magura brakes (for many years the first choice for trials riders) and the more recent Sram hydraulic rim brakes have better modulation than any of the top end disc setups I have used. Unless deep mud is part of your ride or you need rim flex such as in mountain biking, hydraulic rim brakes are superior to discs in every way. Here's hoping the road disc fad dies quickly.
Hydraulic discs self adjust as the pads wear, which may wear significantly during a single race. I have heard that some pros have avoided switching for this reason, however I believe that the main reason they do not is that they are used to caliper brakes.
I would not upgrade to mechanical (cable-actuated) discs since they will not self-adjust, and you may find yourself pulling the levers a lot before the pads engage. I have not ridden a mechanical-caliper bike (cross, MTB or road), so I cannot confirm how they wear.
The improvement in braking performance with discs is too great to ignore. Hydraulic discs have unmatched control, so just go for those.