The base is definitely faster, if you add many resource extractors. But you have a very limited cargo space. I'll try to explain my way of understanding the extraction rate vs cargo space issue.
Once a resource is mined, it's reserved to some customer of your empire or your empire. Once reserved, the resource is basically already paid for until a freighter comes to pick it up. That freighter might take a while to get there, but it doesn't matter for you since you already have the money.
A resource can be reserved multiple times as it gets mined. So an empire can reserve 5000 then 2500 then another 5000, depending greatly on its freighters getting there. At least that's what I've seen.
On a station, only tiny amounts of the resource are reserved, because I think cargo space is taken into account and each customer gets a % of the cargo space reserved, depending on demand.
On a planet, since there is limitless cargo space, each empire gets as much as it wants, as the resource gets mined.
The extraction rate is slower with a colony. BUT until freighters start pouring in, it's basically a reservation game. You get money from storing the resource there for your customers. On a base you have limited space, and so you can only reserve like let's say 10000. On a planet, even if the first freighter takes a year to get there, you'll already have mined 1 000 000 units of that resource, and most of it reserved already. In my opinion that is much better for profits. I might be wrong, but it worked out much better for me, after my SUPER DUPER MEGA ULTRA HIGH TECH CUSTOM MADE MINING STARBASE got whacked by a pirate out of nowhere even before construction. By the time the trade routes were forming I already had plenty of contracts and reserved resource batches lying around, and money was pouring in.
At least that's what I've noticed in my AAR game for the zentabia fluid. I've hardly seen any freighters coming, but there are batches of 2000 or so units of fluid for every empire already there. The colony is in a remote place so that might contribute to the slow distribution. However I have billions coming in already, as you can see from the latest chapter.
3) If the system is already yours the AI will be reluctant to just pop in a Colony out of the blue. Minimum mining bases get blown up by pirates, clog up your warning screen and are a fuss to build for the busy construction ships.
4) You can't always defend a station properly. If the enemy just pops in and focuses on the station, it has a high chance of getting blown up before the enemy fleet is dealt with. And if you're in a war you might not notice among all those battles that a fleet has just attacked that zentabia moon.Also you can't upgrade private mining bases, and starbase class stations don't always work well for trade, also if you build a starbase the planet is not considered owned. I've seen the AI pop a mining base on a planet I already had a starbase on and stealing my mining. That starbase never got visitors as well, so the mining station designation is EXTREMELY important. A colony spaceport can ALWAYS be upgraded.
Besides, resources stay on a planet, while on a base they get blown up with the station. You can always reclaim your planet and the old trade routes. Much less of a fuss.
Of course, I tend to do mixed, depending on my mood and roleplay I have going with the race I'm playing. I'm a base building maniac so I might just be inclined to build a SUPER DUPER MINING SPACEPORT OF DOOM there to speed things up. A colony takes a bit longer to get into the trade circuit.
Hope that helps.