Bomarsund was destroyed completely rather quickly, as it was not designed to resist rifled guns, were not complete and did not take into account that steam vessels could sail and manouvre in ways that sailing vessels could not. Above all, Bomarsund and Sveaborg were isolated on islands - the Entente could alnd guns and men to bombard and attack the forts from the land sides, which they could not at Sevastopol due to the large amount of Russian land forces.
The modern commenter will know in what a sorry state the Russian military was, as was the Sveaborg fortress itself. But what would the Anglo-French(-Swedish) commanders think at the time? Maybe something along the following lines.
Compared to Bomarsund Sveaborg was huge, both in terms of area and the number of men. One could well expect the garrison on the islands alone to be up to 10 times bigger than at Bomarsund in 1856, depending on butterflies. Early Swedish entry might spook the Russians enough to commit much more troops to the defence of the area than IOTL. And OTL, the Tsar for example was afraid that the enemy would try to take Sveaborg and land troops here to attack towards Hamina and Viipuri by land.
And there would be considerable troops and batteries also on land around Helsinki proper. The attacker would have needed to take the town itself to really get at Sveaborg from the north. Considering how careful the Anglo-French were about attacking any settlements in Finland (and how much flak they were getting about it in the press back home), a decision like that would have to be carefully considered.
A lot of the fortifications and guns were old and obsolete, sure. But the islands making up Sveaborg would seem a lot harder to get at than Bomarsund, being a complete fortress system rather than an incomplete one like the latter, even if old and partly neglected. How neglected, they would have to guess. And the islands were surrounded by naval mines, too. Those were not much by more modern standards, but apparently they were considered something of a deterrent even during the OTL bombing of Sveaborg.
Bomarsund was not taken by a frontal assault, it surrendered and was consequently demolished. I think also at Sveaborg the Anglo-French(-Swedish) would first of all expect the fortress to surrender rather than to try to assault it. That could be expected to take time, even if most of the fortifications could be reduced easily.
A map of the fortifications and minefields at Sveaborg at the time: