If a BB keeps it's main gun ammo on board you don't think a CV will keep it's bombs and torpedoes? Perhaps even it's avgas? In any case lighter bombs can cause deck damage to CVs. Lighter means a bomber can carry more and increased the P(H). The BBs proved vulnerable early war at Brest I see no reason to assume CVs wouldn't as well.
But some attacks also pretty much got in free. And how big a CAP can the Germans keep in the air? And how will they deal with night time raids?

AFAIK the danger of ammo magazines is more fom the firing charges than from the shells, shells are designed NOT to explode during the pretty violent treatment they get at firing time and bombs are more similar to the shells than the charges, still moving them around too much is asking for trouble, avgas is comparatively much easier to pump in and out. A CV without avgas on board is no more vulnerable than another ship type, a hit is likely to do more damage to the lighter structure of a CV but also, unless fatal, easier to repair than than the complex armour of a BB, CVs sometimes were repaired in weeks BBs usually took months.
My point is not that the German squadron becomes completely invulnerable, just very much harder to catch, the presence of the fighters turns an aerial torpedo attack from a near sure thing to unlikely to succeed unless a much bigger attack group is sent and that requires a large carrier force and a new doctrine from the British, even if without immagining an all out effort like the attempt made against Tirpitz that was probably a "one shot" affair.
The usual British tactics like the attack on Bismark and the one on Vittorio and Pola at Matapan would have most likely failed with even a couple of fighters present, the Italian though that even a single Re 2000 catapult figher was likely to seriously disrupt the single squadron Swowdfish attack the RN often employed though the theory was never put to the test.
Night attacks in the middle of the Atlantic are not likely to be attempted if a daylight attack still has reasonable possibility of achieving results as the chances of something going very badly wrong (think blue on blue) with a night one are pretty high, based on historical occurrences and tactics the RN is likely to have one or more cruiser squadrons attenpting to shadow in addition to the main CV group. Assuming they do try it, the CV adds very little to night air defence as the 109T has no night capability, improvvised tactics based on moolight or searchlights could be marginallly effective against a shadower but are useless agaist a multi plane attack.

Ah but does it? I strongly suspect that CAP for instance would not have been able to do much to the attack that damaged Bismarck. Visibility conditions were just too bad. If the Germans did have a AA radar and were using it then the British probalby wouldn't have lost them as they would have been able to track the radar.
The British did have radar equipped attack planes by early 42 and a doctrine for using them. Not sure how likely the blue on blue would be...

Don't know about the actual attack but a CAP is likely to rid the Bismark of any shadowing PBY, having some air capability gives the German commander a number of additional options and IMO significantly complicates the task for the Royal Navy.

They came pretty close to hitting Sheffield during the Bismark chase and that episode is likely to make a CV commander reluctant to lanch a low visibility attack if an alternative is available.

Or is it? How long did PBYs shadow Bismarck? Weren't they more concerned with just locating her? Something a CAP may have little impact on. Speaking of shadowing the Japanese float plane at Midway did a prettty good job in spite of US CAP which was a lot better than the German would have been and in conditions that were nominally more favoreable (at least that's my impression) to the CAP.
At least until the first bomb or shell hits her deck. And protecting a CV also adds quite a bit of complication to the German side of things.