Not sure if I understand this correctly....
For example the strike against the ammunition depot:
If you not have any bombs you select the purple target and order your flight to attack it, but you attack vehicles instead?
Hi von Oben,
probably the ammodepot is not a good example because there are only a couple of vehicles associated with the ammodepot. Where the campaign mission target is a larger facility, once you have the target showing on the tactical display, cycle through the different fields of the tactical display. From memory, it goes ALL, aircraft, Vehicles, Buildings, Ships, Airbase (not necessarily in that order). When you can see the target facility, you will see that the purple triangle which is the target/objective for the mission shows up as a Building (so you will see the purple triangle in the ALL view and the Buildings View on the tactical display). In addition to the purple triangle, there is a cluster of red triangles at the goal facility. These triangles are vehicles usually.
So to answer your question, I am suggesting that something like a Spitfire can attack the vehicles associated with the facility, rather than the purple triangle. Sometimes this works to achieve the 100% of the requisite damage required to meet the goal. To be strictly accurate, for facilities, I suspect the purple triangle is not a building, but a nebulous area in the centre of the facility (check out the artillery facility as a target, for example). The way I view the target is to cycle through the F4 views once I've selected the target and it is bracketed.
For an ammodepot, there are one or two vehicles in the facility, from memory. So in the Vehicles view of the tactical display, you should be able to select each vehicle at the ammodepot, and instruct your wingman to attack it (remembering that if there are two free unassigned wingmen, when you press A both wingmen will attack the vehicle). I've modified the stock ammodepot so there is an AA gun at the facility too. ETO probably has done something similar. The AA gun at the ammodepot is selectable under the Vehicles view of the Tactical display.
But overall, I think it would be easier as I said before, for a 1940 era installation of CFS3, to modify the campaign spawns so that the damage required to the ammodepot is down as low as, say, 2%. Then your spitfires or other planes with MGs only and no other offensive loadouts, can attack the target and achieve the goal using MG fire only.