It seems to me that the OP's algorithm is linear in the sum of the thrusters, while yours in quadratic in the number of ships. However, yours wins in memory usage, your memory usage is linear in the number ships, while the OPs algorithm needs memory linear in the sum of the thrusters.

But since the OP says it's just 1000 ships, most of them having a weight of less than 10, I doubt the OPs approach (or yours) should be much of a resource hog.