So the real problem is too easy availability of one vs. the other.
Yes. I guess switching their spots in the tech tree might be a solution. Smugglers offer spikes, seagulls as a bounty prize. Feels right.
Other than that, I think spikes could use a buff in accuracy. Spikes have 35%, airballs 40%. Surely missiles hit better than airballs???
The accuracy is even more important because the early dangerous shippings (the hunterkiller ones) are police and bandits, which mostly have avoid bonus.
To keep the dps from getting too high, lower the fire rate a bit. If you want to go even further, increase the ammo count so a lone airspeeder with a spike launcher is less of a gamble in engagements.
If the regular spike launcher gets any buffs, the Little Ilya might need to be adjusted to make sure it's still better.