Ok, I'll explain a little further:
We have to see two things separate: The games and the lore behind it.
The reason why you can only fly four ships in atmosphere (Hellcat V, Excalibur, Vindicator, Dragon) was limited space on the game discs and limited budget for all those fancy cutscenes the guys at Origin would have had to make. Remember that WC4 was one of the most expensive games of all time. They didn't want to spend even more. WC3 wasn't cheap, either. And it had only 4 discs. So they decided that you could only fly some ships.
I'm quoting LOAF now, for the list of ships:
Wing Commander:
Scimitar - Engage in atmospheric combat on WCA.
Rapier II - Ground support at Vukar Tag in End Run.
Dralthi - Bombs Hurricane in WC1 cutscene.
Dralthi II - Lands on Firekka in Freedom Flight.
Krant - Atmospheric combat at Vukar Tag in End Run.
Wing Commander II:
Ferret - Lands on Ghorah Khar, Novaya Kiev in WC2.
Epee - Visible on ground bases in WC2.
Sabre - Ground support at Vukar Tag in End Run.
Broadsword - Attack Mylon in Wing Commander novelization.
Sartha - Atmospheric combat at Vukar Tag in End Run.
Grikath - Engage in atmospheric combat on WCA.
Jalkehi - Land on a planet in WCA.
Wing Commander III
Arrow - Launches from Sirius on WCA.
Hellcat - Option for atmospheric missions in WC4.
Longbow - Enters atmosphere on SAR mission on WCA.
Excalibur - Option for atmospheric missions in WC3.
Darket - Land on Nargrast in False Colors.
Dralthi IV - Fly into throne room in WC3 intro.
Vaktoth - Fly into Kilrah's atmosphere in WC3 novelization.
Paktahn - Fly over Capitol Building in WC3 losing endgame.
Bloodfang - Fly into Kilrah's atmosphere in WC3 novelization.
Ekapshi - Atmosphere-specific fighter.
Wing Commander IV
Vindicator - Option for atmospheric missions in WC4.
Lance - Option for atmospheric missions in WC4.
I think he missed only one fighter in the list, the Jalthi. It is seen in Freedom Flight over Firekka.
And apart from fighters I think we see a shuttle landing in atmosphere, so although it doesn't look very capable of atmospheric flight it does. And of course the Marines dropship. can land on planets, otherwise it would be pretty silly.
Concerning weapons, I quote LOAF again:
The three guns that aren't effective in an atmosphere, per Victory Streak, are the Laser Cannon, Meson Blaster and Particle Cannon.
... except the atmosphere-only Ekapshi mounts Mesons and Lasers in WC3 and the Hellcat uses Particle Cannons in WC4.
I think that in that case the person who designed the manual mentioned a planned feature that was dropped during the development of the game and wasn't taken out of the manual.
(Similar things happen in a lot of SciFi. If you are a Star Trek fan you might have noticed the inconsistency that they tell you impulse drives don't work in atmosphere (Kira tells you in DS9 somewhere), yet you see ships using the impulse drive in atmospheres in a lot of cases during the series.)
So you see there are a few inconsistencies. Someone also pointed out that in WC4 the mechanic (Pliers) mentions sometimes when clicking on the Vindicator that it is the only one capable of atmospheric flight. But even in that game it is shown that he is wrong, so that is likely to be an error. (Yet there is the possibility that the Bashee really isn't capable of atmospheric flight, and Piers means that of the Borderlands ships the Vindicator is the only one. Quite a stretch, though, I think it is an error.)
Ok, having said that: Take a look at those ships that we are sure to be capable of atmospheric flight.
If all those ships can do it, why shouldn't others? I mean: Some of them don't even have wings and are quite small. We know that they can stand earth gravity and pressure because we see them all land inside the carriers on the flight decks when there are people around.
And if a Paktahn (which is as aerodynamically shaped as a brick) can fly over earth, why shouldn't a Thunderbolt or a Strakha be able to do that as well?
So I come to the following conclusion:
While we don't have proof that Strakhas or Hornets for example are capable of atmospheric flight, it is rather likely, because there are other similar shaped fighters that we know are capable of it.
