Well, first of all, the Ottoman Empire didn't decline. Modern historians have pretty conclusively thrown out the idea that there was a "Decline of the Ottoman Empire." The literature on this is immense, but one can see for example Hathaway, Jane. "Problems of Periodization in Ottoman History: The Fifteenth through the Eighteenth Centuries". The Turkish Studies Association Bulletin 20 (1996): 25-31.

But to answer your question, Malta was mainly a problem for the Ottomans because it was the base of operations for the Knights of St. John, who acted as pirates against Ottoman shipping. Taking Malta would have made all Ottoman travel in the Mediterranean much safer. It would also have made future Ottoman expansion in the central and western Mediterranean possible, but it's worth noting that Malta was already one of the only remaining targets which could have reasonably been attacked. The difficulty of conquering a fortified point was directly related to its distance from Istanbul, from which the Ottoman fleet was launched. This is because more time was required to reach the intended target (leaving less time before the approach of winter), and also because the target would then be closer to the Spanish bases from which relief efforts were organized. This is fundamentally why the conquest of Rhodes and Cyprus was successful while Malta was not. An attack directly on the Spanish bases in Sicily, or on the islands of the Western Mediterranean, would have been incredibly risky and unlikely to succeed. In this light, I think the idea of Malta having prevented the Ottomans from advancing into Europe is more closely tied to legend and myth than to reality - after all, many writers have wanted to portray the Ottoman-Habsburg conflict of this period as a sort of Early Modern "Clash of Civilizations" in which every battle was about stopping the "Tide of Islam" or something like that. The reality was much more mundane: Malta was a glorified pirate base, and the Ottomans wanted to eliminate it.

On this see Guilmartin, John Francis, Gunpowder and Galleys: Changing Technology and Mediterranean Warfare at Sea in the 16th Century, 2nd ed (Conway Maritime Press Ltd, 2003).