Unfortunately I can't say I know what was going on in the head of the Venetian commander (Francesco Morosini, who would later be elected Doge) as Venetian shells set the Parthenon alight, or if it was an intentional target or not.

But it might be worth considering that a recognizably "modern" attitude to historical preservation in Europe wouldn't emerge for nearly another two centuries. Early Modern Italians, like most Early Modern Europeans, could have a surprisingly flippant attitude towards structures which today would be recognized as valuable archeological ruins. Across Italy (and Europe) ancient structures were habitually repurposed, dismantled, and incorporated into new structures with little regard to historic conservation: as an example, the Roman Colosseum owes much of its current state to having been first turned into a fortress (much like Hadrian's Mausoleum, perhaps better known as Castel St. Angelo) subsequently destroyed, haphazardly turned into a church, and ultimately used as a quarry. Just the same way countless Ancient Roman Structures were repurposed (in Rome they were typically but not exclusively converted to Churches) the Athenian acropolis at the time of the venetian siege would have been hardly recognizable compared to its state today, as a significant number of its medieval and early modern structures were demolished after Greece's independence. So while Morosini might have been fully aware of the Parthenon's history, it is possible that he primarily thought of it as a disused mosque storing gunpowder, or more banally, one of many buildings (some ancient, some more recent) which crowded the Acropolis where the Ottoman garrison was perched.

This is not to say that Early Modern Europeans didn't value historical buildings and artifacts (the looting of the acropolis by the Venetians after the siege is proof enough) only that their attitude was much different when compared to modern attitudes. Venice itself, while today one of the best-preserved historic cities in Italy, in Morosini's own lifetime would see palaces along the Grand Canal and elsewhere in the city demolished or extensively remolded, with older, outdated structures replaced by newer ones with inconsistent attitudes towards preservation. Indeed through previous centuries important structures like the venetian Doge's palace had been built over the foundations of older demolished buildings (the airy late gothic/early renaissance building replaced a more austere Romanesque castle). And of all the large cities of Italy, Venice is actually alone in having absolutely no Greek or Roman architectural heritage at all, which means that while Morosini and the Venetians laying siege to Athens certainly weren't oblivious to the existence of ancient ruins, they wouldn't have had any real experience considering the matter as far as their home city was concerned, nor would they have an analogous local structure to which they could compare the Parthenon and perhaps conclude they ought to exercise more caution.

And lastly, Morosini and the venetians in general were fairly ambivalent towards the Republic's Greek possessions, especially where they had weak preexisting social and economic ties; the Morean War was more geared towards enhancing the Republic's prestige and scoring a blow against the Ottomans rather than preserving trade routes or economic interests (which were at this point well on the decline). So first and foremost Athens was a military target, an objective in the war against the Ottoman Empire, while in the past communities were Venetians had stronger social ties might instead have been besieged with more caution. This means that there is no scenario in the siege where Morosini does not bombard the acropolis, and even if he didn't expressly target the gunpowder magazines in the Parthenon, the probability of shells hitting the building would always be very high.

While the impetus to construct museums in Italy would grow rapidly after the country's unification (although it did have clear pre-unification origins) and architectural preservation would develop soon after, the use of architectural heritage and preservation to develop emotional bonds linked to shared heritage, history, and identity was very much a feature of the industrial era.