My understanding of the Hood is that she was probably better protected than any of the pre war designs due to sloping armour. Also that the suggestion that she was lost due to a shell detonating in her magazine via belt or deck is now considered unlikely. The most likely current theories as to her loss relate more to issues with the ammunition for the 4” guns which were added post completion. Thus her loss could be considered more of a fluke and no more likely to occur than in any contemporary ship.
I've attached what is I think the most recent and definitive analysis of
Hood's sinking (and also
Bismarck's). This was made following the 2001 expedition to the wrecks with ROVs. In the attached file, the analysis of
Hood starts near the bottom of page 14, although the rest is quite interesting, too.
You can find photos of the wreck, here:
http://www.hmshood.com/
and a highly recommended 2007 analysis of the sinking here:
http://www.warship.org/no21987.htm
Anyway, from the wreckage, it's quite definite that the whole 120 tons of cordite in the aft magazine group (4" and 15") exploded, obliterating 85m of hull from just aft of the 2nd funnel to just aft of Y barbette. As you say, the 4" magazine most likely went off first, but it was (in theory anyway) just as well-protected as the 15" ammo. It was under the same number of decks and behind the same belts, on the centerline. IOW, it's protection was nothing like the dangerous arrangements of WW1 RN secondary magazines.
It seems most likely that the fatal shell actually exploded in the 4" magazine and not outside it, based on experiments done with shooting at mock-up magazines. There are several paths it could have taken to get there, depending on how far into her final turn
Hood was at that moment. Her rudder was found hard aport so the turn was in progress and
Hood would have been heeling over towards
Bismarck, decreasing the striking angle on the decks but increasing it on the belts. As such, it seems to me (and those who examined the wreck) most likely that the shell came through the deck of the after engine room, which was thinner there than elsewhere. Because
Bismarck was still on
Hood's starboard bow, the shell would have traveled a bit aft of its point of impact, probably through the common bulkhead between the engine room and 4" magazine. The 15" magazines were adjacent to the 4", so they went off in a chain reaction.
Here's page 4 of the above analysis, which shows the likely sequence of events drawn on
Hood's plans, about 1/2way down the page:
http://www.warship.org/new_page_2.htm