Thanks for all the suggestion. To sum up the advice from this thread that I will be using, and summarize the current design:
1) Missiles won't be devastating nukes that kills in 1-2 shots anymore. Instead, they just do a lot more damage than guns/lasers, and hit 100% of the time (no chance to dodge). Guns/lasers miss x% of the time depending on the size of the target.
2) The trade-off is that ammo is limited, you need to sacrifice a gun/laser mount/slot to equip a missile launcher, and the missile takes (for example) 1 turn to reach the target while guns do instant damage.
3) Another trade-off is that the target can equip ECM or other anti-missile technology to give it a X% chance to reduce missile damage significantly (or dodge the missile entirely).