I use the smaller hull sizes for boarding ships, troop transports, point defense ships and minesweepers. Non-combat ships use the size best suited to their role. For instance a ship used to drop spy satellites rarely needs to be larger than an escort.
Regarding the front line ships:
- Boarding ships: I find a light cruiser to be just the right size. Allows a couple shield depleters, a shield and a couple boarding parties. No need for more.
- Troop transports: Again the light cruiser. In some mods (ie: Proportions) you do need the huge transport but in most mods 1200 kt cargo space is plenty.
- Point defense: I usually use one or two sizes smaller than my largest ship. Rather than have the PD concentrated in one spot, I like to spread the guns around.
- Minesweepers: A single base ship minesweeper is all you need, but lose that and you have none at all! I prefer several smaller ships and even then carry 50% extra in a fleet. The loss of one or two is not critical, just annoying.
To blockade a planet I find it safest to use unarmed ships.