First, commerce does not really convert freight into goods, they just use freight to increase their happiness. Therefore, goods appear at 6am/pm automatically per commerce (In more detail it depends on the type of commerce two 12h shifts or only one 12h shift per day). But that was not your actual question. Pre patch 6 (I hardly played that game since then although I got the addon as a present on my birthday) a single low dense/wealth resident was able to emit a shopper 2 or under perfect condition even 3 times a day, which a guy in the official forum has calculated once, which lead to spending all the cash the workers (if all managed to bring home 3$) brought "home". But as 3 times a day is really hard to achieve, a shopper should be able to go out 1-2 times a day.
Not sure if Maxis changed something on the way shoppers (or agents in general) act, but shoppers used to head for the nearest "home" of their wealth level which has an open spot for this type of agent AND requires happiness! If there is either no house of the agents wealth level with an open spot for this type of agent or if no resident of this wealth-level requires happiness, the shopping-agent will leave the city. This was somehow an important finding as up to this the overall impression was they just go for the nearest "home" but on the other handside plenty of agents left the city with money/goods in their pockets.
The way agents move in the game is triggered by a utility-function which integrates the distance to a location and certain factors like i.e a shopping agent after having done some shopping, the utility function will consider the happiness value of residents of the agents wealth level. The spot that yields the highest utility will be the target of the agent. Therefore multiple nearby agents may compete for the same spot.
The number of times a shopper is able to shop depends on a number of factors. As already explained above, under perfect conditions they could even go shopping 3 times a day if enough money and goods are available and if distances are short. As megatowers seem to be "near" enough, your shoppers seem to be able to do their shopping at least twice a day. The point however is, that a shopper coming from a residential area inside of a megatower might not be returning to this location again as maybe 4 blocks away there is a house that requires plenty more happiness and therefore the utility-function will carry the agent to the farther away resident.
As there often could be multiple reasons for the actual behavior of an agent, it is quite hard to really tell what is going on. Furthermore, Maxis limits the amount of information given to us which makes explanations to a guessing game.
