I had considered something like that myself at one point: "Hey, if I just put one troop module on each of my ships, they'll still be pretty effective in combat and I won't have to worry about escorting them or having the computer wiping out a stack of undefended transports. Plus, all of my fleets will always be able to invade." Problems there are:
(1) any ship you lose now will also mean losing troops. True, you are spreading your eggs into more baskets by diving your soldiers among more ships, but it's generally not too big of a deal to keep defenseless transports away from the AIs. With the latest patch, there's no more "first strike" so you will be losing more ships in combat, and therefore, more troops.
(2) as others have said, you lose tranports in the invasion attempts. If I recall correctly, you lose any transport that can't be completely filled up with soldiers after the invasion. So, let's say you invade with 5 armed ships each containing a transport module (so 2.5 billion troops total). Now let's say at the end, only 900 million survive. Bam, you're out 4 of your 5 ships (there's only enough to completely fill one ship with 500 million soldiers). Not only do the base hulls cost more than a cargo hull (smalls cost the same as cargo right?) but you also lose all the extra cost from the weapons and defenses (defense is very expensive) that you put on them. It'd be a very different story if your transport ships didn't magically disappear during an invasion (and personally, I'd prefer that you didn't lose them), but as it stands right now, it seems like quite a waste to me.