If you only have Troop Transport Bays, it means that your forces will be deployed over days, not minutes. Cargo Handling helps speed it up. It doesn't matter much for a planetary assault, as combat is resolved only during production phase, so every 5 days. As long as your transports can fully unload themselves inside that time period, they will function well enough. Otherwise, only some of them will be ready to fight and the enemy might have a superiority of numbers. Whether that matters or not, depends on their tech level and the number of battalions they have. And you can't really see that beforehand.
Bombarding enemy ground forces with missiles is a valid tactic, but beware of collateral damage. It is always immense, even if you only use few missiles. Millions will lose their lives, and facilities will be destroyed. Radiation levels will rise and dust will be thrown into the atmosphere. Generally players who want to loot an alien race, avoid bombarding it.