There is no guide I am aware of but also not needed
Agree with the above: there is no clear counter mechanic here just small modifiers. All weapons (except for Ion weapons and energy torps) are usefull in most cases and the loadout is usually not determined by the enemy faced but rather on:
1. What faction you are playing (and which ships you find visually pleasing
)
2. What tech bonus have been aquired during the current game
The faction played is bar far the most determening factor. In some cases the ideal loadout is more-or-less obvious like in case of Tinkers, but even in their case one can still play aroun with proportions of rocket, torpedo, Leech, EMP and Plasma Torp
In most other cases though, even within a given faction, one can choose 2-3 preffered tactics by utilizing the appropriate layouts (a good thing)
e.g.: Phidi can choose to concentrate on missile/torpedo spamming, carriers and boarding just based on their own designs but when they start buying mercs, they can practically go with whatever they want.
As always, Humans get the most limitations here as well as energy weapons tend to need a lot of modifiers to become competitive (except for ion weapons as they lack most of thes modifiers) but once they are, they are just as valid a choice like the others
Generally I find the best approach is to build a balanced fleet with 1-2 dominant types of weapons + everythign else I can equip on my favorites types of ships. Refit is expensive (or time consuming) and one cannot ract to other loadouts anyhow (that would also require research investment)