Fighters are VERY IMPORTANT in Battlefleet Gothic. One can't just think of how much damage you can do to the enemy ships with the fighter, one must consider how much damage you can prevent to your own ships with the fighter counter. Fighters remove an enemy ordnance counter on a one for one basis.
One fighter removes one bomber, one fighter, etc. and most importantly one fighter removes one torpedo salvo regardless of its size. Fighter even remove orbital mines. Now, another important fact. As clarified by Andy Chambers it doesn't who moves into who: when an ordance counter or ship touches an ordnance counter you reslove the effects of that contact. Hence you may place fighters in front of your ships stands (as a form of CAP) facing the anticipated direction of your enemies attacks by ordnance. Example: Its your enemies turn, his ordnance will move first, however you positioned fighters in front of your ship along the path of his anticipated attack. They manuever a 6 strength squadron of escorts with torpedoes. That 12 strength torpedo salvo goes "poof" as soon as it hits your fighter counter. Likewise, enemy bombers and assualt boats will go boom if they cannot pass between your fighter counters positioned in the path of their attack. Now, they may not have the range to manuever around your fighters and hence you have saved your ships from damage. In order for your oppenent to remove your fighters from their CAPs they must resort to gunfire (now they won't be shooting at your ships) or use their own fighters to exchange one on one which means less bombers and assualt boats to attack your ships.
For the question of whether or not to include fighters in with bomber or assualt boat waves is a question of tactics. If when you launch ordnance they will be able to hit their targets that ordnance phase then the answer would be no. Only use the number of fighters neccessary to remove his CAPs to ease your own attack runs. If you anticipate the ordnance having several ordnance phases to move before they reach their targets then I almost always include some fighters in the waves or flying along in support. If traveling long distances your ordnance counters will likely pass enemy ordnance along the way and having fighters will give your attack craft some protection or allow you to attack some of his waves and weaken them. This gives you tactical flexibility. Obviously, if your opponent has no CVs then you have no reason to use fighters and just pour on the attack craft.
In our gaming group we feel that carriers (and their attendant attack craft) are queens of the battlefield with other ships acting in support (just like the lessons taught in the Pacific in WW2, imagine that). My initial launchings of ordnance will almost always consist entirely of fighters, especially if I was able to move first. My objective is to secure aerial superiority through waves of fighters swarming his ordnance and then start to sneak individual waves of bombers or assualt transports thru (I've found that a wave of at least four will result in some damage on their target) once I've established superior numbers of fighters on the battlefield.
Good luck and good hunting!