Have you actually worked it out using your figures?
Your Siege Cannon doing 3 million damage every 5 seconds would equate to 12 million per 20 seconds (this being the time the Base Repairs itself)
Now with a Shield the damage is reduced by 97% which equates to actual damage of 360,000 damage every 20 seconds.
A Core 4 Base, with all 3 Repair Materials, can repair itself of 720,000 damage every 20 seconds.
Using your damage you will need 2 BSs with 1 Siege Cannon, each, to overcome the Repair capability of the Base.
A third BS with 1 Siege Cannon will then deal damage to the Base.
A Core 4 Base has 24 million Hit Points.
That third BS will deal 360,000 damage every 20 seconds to the Base. The Base will be destroyed in 22.2 minutes (granted the Ships would need 267 Projectiles each).
Lets add a fourth BS. The Base will be destroyed in 11.1 minutes and each ship would need 134 Projectiles each.
The Fifth BS would allow the Base to be destroyed in 5.55 minutes and each ship would need 67 missiles.
The cost to the 5 BSs would be travel time + 6 minutes + 3,350,000 credits + the cost of the Siege Cannon.
I haven't even bothered calculating for any Base less than Core 4 as it would be a complete waste of time.
'I would like to be half as clever as some people like to believe they are' Life is full of disappointments, it is how we handle them that helps to define us, as a person