The decision about which weapons to research and put on your ships is a fairly complex one and one whose inputs change as the devs tinker with them.

The screen snapshots below show the capabilities of a beam weapon(Plasma Pod), a missile weapon (Avenger), and a kinetic weapon (Pulse Cannon).  These capabilities are the same regardless of which size ship you put them on EXCEPT for frigates which, for some reason, have higher accuracy rates (140%, 100%, and 117%).

Ranged Attacks

You are correct that missiles have an advantage outside of combat in that they can launch a missile attack at an enemy ship or fleet from up to 3+ tiles away.  However, the devs have also given that capability to beam weapons, but at a reduced range.  The kinetic weapons do not have a ranged attack capablility.

Combat Abilities

When you get into combat, the different weapons have some advantages and some disadvantages.  For example, missiles are able to fire at the longest range (5000 km), but with low accuracy (50%).  This means that they can possibly destroy their target before the target can fire back but, if they do not destroy their target, they will have to wait 5 cycles to be able to fire again.

Once you get within range of beam weapons (2000 km), their greater accuracy (90%) and cooldown rate (3 cycles) means that they will do more damage than missiles.

Once you get within range of kinetic weapons (500 km), their ability to fire every cycle makes them very deadly.

The table below shows the damage done over 15 cycles once all ships are with 500 km.  The formula is:

Damage = (15 cycles / cooldown cycles) * accuracy * attack power

This analysis excludes the effect of defensive measures the enemy has put on their ships which are unknowns for the purpose of this analysis.

Conclusion

I think the devs are doing a great job of tweaking the strengths and weaknesses of the 3 different weapon systems.  Yes, missiles are great for ranged attacks before combat and, yes, they get to fire first when they do enter combat, but once the ships get within 500 km nothing beats kinetic weapons.  Beam weapons are a middle of the road choice because they can also do ranged attacks and their accuracy and cooldown put them in between missiles and kinetics.

Should you go with all missile weapons?  All beam weapons?  All kinetic weapons? Some combination of 2 or all 3?  That is a lot of the fun of the game!  Trying to decide what ships to build, how to equip them, and how to combine them is fun and nerve-wracking until you see how they perform against different types of enemy ships and fleets.

Note To The Devs

It is clearly an advantage for ships with only missile weapons to get within 5000 km, fire their missiles, then move outside 5000 km for the cooldown period, then go back within 5000 km to fire again so that they can fire while minimizing the risk of being hit by enemy weapons.  However, there does not seem to be any intelligence built into the combat engine to implement this obvious strategy. Ships with beam weapons should want to stay between 2000 km and 500 km, and ships with kinetic weapons  should want to race in to within 500 km and stay there until the end of combat.  I do not know how hard it would be to implement this positioning strategy, but it is something to think about.