Well, that depends on how much ships you will need to overcome planetary defenses.
If, for example, planetary defenses are able to inflict at least some losses to an attacking small or medium-sized fleet, this will reduce the advantage and speed of an attacker.
It would also make it impossible to send off an armed transport or a transport an two or three tiny ships to capture a planet on their own.
However, it will not (and should not) prevent you from sending five capital ships before you send in your transports.
In my opinion those "fast transports" should be nerfed too.
It is simply ridiculous that engines do stack. This is simply wrong. Using two or three engines will not allow you to be two or three times as fast as before (as is proven by simple physics).
What is more, it is likely, that your ship will not be able to stand the force of additional engines without changing the design of the ship (additional stabilizers, walls and so on).
Last, but not least, it is simply bad game design to allow people to min/max their ships in such a way. It leads to "gamey" ship designs. No real general will decide that he wants tanks that do not survive a single enemy hit, even if this allows for greater speed of movement or for more weapons, because it will be catastrophic for the morale of your troops.
In GalCiv3, you can "throw away" the lives of your space-pilots without any thought. Simply build new ships and recruit new troops. Nobody will ever ask what happened to the old ones.