Probley an easy question to answer.. but

[Gryphin]

comisar (and others),
A colony ship does not *need* a cargo bay. If you include one on a colony ship it will move more people, (see the thread on "what good is population).
If you are going to settle in hostil territory, you can fill the cargo bay witn troops or other units and they will be deposited on the planet and available for defence. You caould also drop said units off somewhere else along the way if you wanted to.