How is the attacked fleet selected

As fbueckert notes, you only start "wasting" food once the entire system is fully populated. Beyond that, extra food isn't very useful. There is one improvement, late in the East technology tree, that converts 100% of surplus food into industry, but you're much more likely to fully population cap systems before you make it to that point.

Two things that bear consideration, however, are Colonists and +Pop system improvements. Making a colony ship will actually remove one unit of population from your system (just as scrapping a colony ship will automatically add one population to the nearest star system, if possible). In the short term, you can use the population-capped system to produce colony ships, and though I don't know the details, it seems that some food and production are stored, such that if a population capped system produces a colony ship, the planet will immediately regain its lost population from the "wasted" turns. (Though, again, I don't know the exact mechanics)

The other thing you might want to consider is are the +Population improvements, the earliest of which is Endothermic Structures (+1 to small, +2 to tiny). As soon as you build one of those structures, the population cap increase, and you will need food production until you max out again.

Neither of these are permanent solutions, however. The only consistent use for wasted food is from the End-Tier, "Dust Virtualization" tech.

Fleet size is determined by Command Points Cap, found on the left (Diplomacy and Trading) branch of the tech tree.

Clicking on a fleet and looking at the number next to the satellite dish icon is a quick way to see the fleet size limts. Here 16 of 16 slots are used.

Note: Researching Quantum Communications unlocks C3 Systems which gives you +2 cap for each new ship class acquired (ship classes are unlocked in the bottom tree, Exploration and Expansion).