Just a few purely technical issues:
Gontzol guide is good for its time of arrive, just better to keep in mind what its only roughly 70% true, and info about some basic mechanics like Beam and Missile Attack is wrong. Definitely worthy reading still though, as many info are systematized well there.

Thats not exactly correct. If one can have problems with hitting opponent's ships with Fusion beam from the distance, so suffering dissipation and also additional to usual range penalty (as its Fusion), then thats quite possible what without any range penalty, any dissipation, and with +1 damage and additional 50 beam attack from fighters - there will be totally different outcome (assuming 1.4 classic rules here).

Likely mistype; "AF triples damage" (more precisely AF does 3 shots, while ENV do a damage 4 times (if it just quadrupled damage instead - it would be able to kill only one missile per cannon, not up to 4)).

Dedicated anti-missile ships are very good, especially against AI, as AI just fire missiles from the distance and unable to effectively use pointblank shots.

"- For beam ships/mid-game: what weapon would be your choice to replace fusion beam/mass driver?"
Generally nothing is really needed (assuming classic game settings) after EMG missiles. Late heavy beams let player even to skip a need to actually move ships tho.

I have no idea which parts of Gontzol's FAQ are accurate, so the following may not be correct:

If you are using Fusion Beam, you want to tech-up till you get the enveloping upgrade (ENV) for 4x base damage (or rather 4x # attacks as DarzaR states above). Gontzol's FAQ is pretty clear that unless you have High Energy Focus, "normal" beams do 20% more damge than "PD" beams for damage output per same space required. SO you want to use normal Fusion Beams with the CO ENV upgrades for 6 x 4 = 24 base damage per gun at range 0. Thus 1 successful hit will destroy 2 normal pulson missiles or 1 ARM pulson missile (at range 0). Range dissipation should be about 20% per 3 squares using normal FB.

IIRC, the final miniaturization step for Fusion Beams comes at the "Artificial Gravity" level tech. SO you still might want to research Gravity Generator or Graviton Beams, even if you are still using Fusion Beams as your main armament. Starbases and Ground Battery auto-upgrade to the highest beam tech available. So sometimes you might not want to get Graviton Beam if you prefer miniaturized ENV CO Fusion Beams on your Starbase.

Per Gontzol's FAQ, each anti-missile rocket has a base chance of 60% interception at range 0, with decreasing chance at longer ranges. So you could expect 6 AMR to take out ~4 pulson missiles at 0 range, or fewer hits at longer ranges.

BA = Positronic + Battle Scanner + Normal Crew + CO Bonus = 75 + 50 + 15 +25 = 165.
BD (for missiles with Anti-matter drive) = (Base Speed + Drive + Fast) * 5 = (10 + 6 + 4) * 5 = 100. Not sure if racial picks affect BD for missiles.
Per Gontzol's to-hit table: BA - BD = 165 - 100 = 65 ...so... ~95% chance to hit a missile at range 0.

Thus 5 CO ENV Fusion Beams are likely to take out at least 4 ARM pulson missiles or 8 normal pulson missiles at range 0. Another advantage of using Fusion Beams rather than AMR is that FB can attack other ships, starbases, fighters and non-shielded planets too.

Probably so. But it also might just be better to use that space for more Fusion Beams, so as to gank enemy missile swarms before they can hit your destroyer fleet. Jammers won't help a glass-cannon much, but they do make tanky ships harder to kill using missiles. Check out Gontzol's FAQ for the numbers.

Nah, Fusion Beams work fine for missile defense once you get the ENV modification, as long as you can get in close enough so range-dissipation doesn't reduce damage too much.

Manual for patch 1.50 have a good coverage for most of mechanics you mentioned there, so instead of pinpoint corrrections - i suggest you read it there as a whole.

While many ones preferred such fusion beams on their Starbases, currently such things are impossible in moo2. Miniatutized - yes, ENV CO - no. Ground batteries have some additional mods tho.

@ Dreamteam67

Very impressed with the effort you put into these answers, feel I have a much better grasp of things by now.

CO ENV fusion beams are available to me and look like the superior option in my current situation. I also like that such a ship is more versatile than a ship fitted solely with anti-missile rockets.

My spies managed to steal the ECM Jammer, and I have retrofitted my ships with it. I feel the space it takes up is modest enough for me to spare.

@ DarzaR

Hmm, I am playing ver. 1.40b23 (the GOG-version). Could be I should look into patching it. Have you been involved in putting the patch together? I had a look at the readme and noticed it was signed by "Darza" :-)

Yes, Darza is most certainly part of the 1.5 team.

Good for a start, but i meant Manual here, as it include some stuff about game mechanics too, particularily ones you asked about, and its better to read about them there, instead of Gontzol's (while its better to read Gontzol's too, sure). That not directly connected with using 1.50 patch or not using it.