And yeah, I also want to echo the others who have said that missiles are not the ultimate weapon that trumps all else. It is very much possible to create Point Defence thick enough that missiles cannot penetrate it in any reasonable scenario. Over in the Ship Bureau, there are designs for the so-called FlaK barges, which are cheap railgun platforms that can be built by the dozens and will. That's just one example. In the Fiction sub-forum, you can find tales of how human PD defeats all incoming NPR missile salvos.
Yes, PD are very effective against regular sized missiles fired from normal sized launchers. NPR almost exclusively use that on normal ships and mostly use box launched ones on FAC and fighters only. When you play in games where the designs are created by human hand on both sides it becomes a bit more tricky as you might face a combination of box launches, reduced size launchers and regular launchers so it is harder to tailor the PD to a specific type. In VB6 there also are the issue with fire-controls which can be abused as well.
Now... I don't think that we should encourage highly abusive tactics either. Using 3BP rail-guns as PD are probably as abusive as using fire-controls or different missiles in one fire-control to get multiple salvos from one fire-control. Another way to completely abuse missiles are to create a missile (MIRV) who have the same speed as your ship, collect all missiles in the inventory in one giant salvo, completely horrible abuse of the mechanics. There are also ways you can trick PD firing at armoured missiles before none armoured as there is a strict order missiles are engaged by PD, don't remember exactly what though.
When we look at the balance I think we need to cut the extremes on either side as anomalies as most players probably house rule against most of them anyway.
When you look at roughly same level technology and you don't abuse either beam or missile mechanics then beam weapons can for the most part deal with normal sized launchers quite effectively and will struggle quite severely against box launched or reduced sized launchers. But if you then combine the PD with Shields you can make missiles quite expensive, throw in decent AMM and it is even better, but now you also invested allot into missile defence... in an environment where there is a human designing ships on several sides then designs are usually built and formed along what the enemy has so you can't blindly rely on either missiles or beams as it depends on what the enemy has.
But with that said, missiles are king at deliver high damage from great range.
You can build impenetrable fortresses around a planet with cheap PD but I have never found that to be a sound strategy in my multi-faction campaigns as planets are immobile and there are no real point attacking a planet or colony from long range, most often I don't want to radiate the planet with them either. The best solution is to bring a fleet strong enough to weather any missiles on the colony and destroy it with overwhelming beam weapons and/or bombs. That is why a very strong beam defence is more important on planets and probably even more so in C# I believe, beam defences are allot more costly and those cheap PD stations are pretty much useless in that scenario. In VB6 you start dropping "bombs" at point blank range on PDCs, bombs also are allot cheaper than regular missiles.
This is why I think that the whole discussion about missiles and beams are pointless. Just because missiles in general are king at ranged combat and therefore space superiority does not mean that you don't need beam weapons, you do as missiles can run out... can be costly to replace and upgrade and are not good in all situations.
I just don't understand why it is so hard to accept that missiles are better at some things and beams at others. A fleet that uses a wide variety of weapons and defences also utilise resources and mining production more efficiently, that should not be underestimated. A fleet that is purely focused on missiles will heavily tax an industry in a really bad way as one example, the same with an industry that rely on one type of Beam weapons.
There is nothing wrong with focusing a fleet on one weapon system, especially if it could neutralise an enemies strength a great deal. You also do it for role-play reasons as factions have limited research capacities or just favour a specific system for one or another reasons... perhaps based on previous experiences and so on. I for one try to play all factions somewhat differently and base their wants and needs based on experience and not my knowledge of the gaming system, so they have to learn the hard way.
