"Incompetent" is a joke--I just wanted to emphasize that he was not whitewashing them. 'Stubborn psycho-crusaders' is probably a more accurate description of Crowley's story. My current guess is that there was an equilibrium in the Indian Ocean where war was discouraged by the sheer profitability of peace, so that there was less state-subsidized military innovation than in Europe, where states invested heavily in military technology. Also, while not explaining why the Portuguese had like longer-ranged canons, the fact that they were not on home turf really did allow them much more military flexibility, so it is not like their success was completely tech-determined.
Portugal had Caravels and Galleons.At sea they always won againt non-european adversaries.They only held ports protected by forts that were guarded by hundreds of men with guns.If sieges were already pretty difficult to do if you did not have enough artillery,imagine how hard they were if your enemy had guns with an high firing rate