The calculation you did doesn't factor in the value of the Pokemon. In order to maximize profits, one must catch Pokemon as fast as they can. As the value of the Pokemon that are being caught increases, the time that is spent trying to catch them becomes worth more. Certain rare Pokemon like Eevee, Bulbasaur, Charmander, etc go for 10-20k on the GTL with bad IVs, at the time of this post. Say that they are going for 20k for example. If I can catch them in one throw with an ultraball but two with a pokeball, I'm going to be making more money per hour by using ultra balls. And to put it simply mathematically, assuming catching a Pokemon worth 20k is 1x as fast with a pokeball, and 2x as fast with an ultraball (which I have observed is the case with Bulbasaur). If I use a pokeball I'll get (20,000-400)x1=19,600 units of money per unit of time, while if I use an ultraball I'll get (20,000-1,200)x2=37,600 units of money per unit of time. This example clearly proves that the ultraball, in certain cases, can yield more money per unit of time/hour than the pokeball when catching Pokemon. This is assuming that it takes 2 pokeballs per catch on average and one ultraball per catch on average, respectively. It also assumes that the unit of time=1, and that the value of the Pokemon is 20,000 units of money.
