During the Indonesian War of Independence (that was a very messy thing) the Dutch actually had proposed a very loose structure for independent Indonesia that the mainly Sumatran and (especially) Javanese nationalists rejected. If I recall correctly, some parts of Sulawesi also had centrifugal movements. The country in plenty of distinct groupings that can offer a springboard for a national constructions both on a geographcal and/or ethnolinguistic basis, all further messed up by religious divides in some eastern island groups. Java itself may split along the linguistic Sundanese/Javanese divide, that would leave Jakarta in a somewhat odd position, not to mention the Madurese-speaking area near Surabaya. In Sumatra at least Aceh is very likely to separate from the rest of the islam, possibly the Minang and maybe Batak land too. The rest could stay as independent "Sumatra", join Malaysia, or even split between these two entities. Not sure about what the Lampung area would do. Kalimantan has high chances to become a mess within the mess. If nothing viable emerges from the collapse of Indonesia, Malaysia will take control of the Strait.
Sulawesi would likely split into independent Minahasa, Makassar/Bugis area and Tanah Toraja at least. Bali and Lombok can be independent, the rest of Lesser Sunda probably another mess, with Australia probably running the show by proxy (that could be inviting for anti-western Islamic groups if they can find local hosts). Papua provinces may reunify with Papua-Niugini, and possibly some ot the easternmost islands will join too. Moluku is quite a wild card, probably will split into two states centered on Ternate and Ambon respectively, or stay loosely united in a rather unstable and probably loose union.
Timor Leste will probably go not so differently from OTL.
The whole thing has good chances to be nasty, bloody and confused.
However, widespread piracy in that area is not something that either local and global powers would tolerate for any long. China, India, the US, Australia and Japan, possibly Saudi Arabia and a lot of pissed off neighbours like the Philippines or Viet Nam will intervene rather quickly, or refrain to do so at their peril.