The trick to this achievement is sniper towers. The snipers will destroy ore transports and thus slowing down the construction time.
As soon as the mission starts, one CN to top left island and two CNs can land on the main island together near the lower right transport hub. A well placed nullifier will destroy both this and the nearby spore tower. A blaster cannon will be needed to defend the nullifier. Alarms will go off and CN health will go down, but the nullifier will do it's job before you lose a CN.
Once it does, move a CN to top left island to help over there and the other should go to lower right island. Keep in mind that there is spore tower and each island should have a beam tower!
Whilst all the above is happening, on the top left island you should build a mortar and sprayer. Pretty soon, you should be able to destroy the emitter at the top left and put a relay to the island chain on the right of it (where a ship is collecting ore). A sniper on the new Power Zone and many more around the bottom right of this island will destroy the transports giving you more time.
Using the same tactics as the top island, destroy the emitter on the bottom right and use the PZ with a bertha.
The bertha will help in establishing a relay link from the island chain at the top from your two CNs to the mainland. I used a sprayer and the bertha at the same time to create a relay here. Forge build/packet speeds helped here.
With a relay down, mortars and cannons will let you first of all destroy the second spore tower which you can now place a cannon on. Keep advancing with more cannons until you clear a bit of creeper enough to put enough nullifiers in place to destroy the remaining transport hubs. Don't worry too hard about the emitters: as soon as all hubs are destroyed the mission is complete.
And throughout this mission if you find you don't have enough time, it's because you didn't have enough snipers destroying those transports.