Similar to max mining yield fits, sure you can increase mining yield or cargo capacity but only at the cost of less tank, lower speed and higher alignment time than you could have with another fit. Since cargo ships (and mining ships) are primary gank targets I've always felt making my ships harder to gank is more important than increasing cargo capacity (or mining yield).
Cargo expander mods reduce speed and structure hitpoints, cargo rigs reduce armor amount. All of which reduces your survivability. In addition for every cargo mod or rig you fit that's one less mod or rig you can fit to increase tank or improve speed and/or alignment time.
Nanofibers in the lows increase speed and lower alignment time. You can also fit a Damage Control in one of the lows (DCs don't stack so 1 is all you need) for better tank too. And of course if your ship is armor tanked the lows are where your tank mods go too.
Fitting for higher speed and lower alignment time rather than cargo space means gankers have less time to target, lock and kill my ship. Fitting heavier tank means when they do manage to target, lock and fire upon me, it takes more damage to kill me, which in turn means it takes longer to kill me and I have more time to escape.
I prefer Minmatar ships for transport because they're fast and agile shield tanked ships. Shield tank mostly uses mid slots leaving the lows open for mods to further improve speed and agility.