Hi cwan!
I guess it just depends on what kind of diving you like and is there anything specific you would like to see?
Diving in Dumaguete/Dauin coast in September/October is very nice, especially if you are into octopi. September-October is a mating season for many octopus we have in the area (blue ring octopus, mototi octopus, mimic octopus, wonderpus, coconut octopus, white v octopus and day octopus) and they are “out and about” more than usually, also easier to photograph. I included the photo from last year, all photos taken by our in-house marine biologist Daniel within a couple of days in early October.
And then there's coral reefs of Apo Island nearby too (around 25 minute boat ride from our place, more when you are staying closer to Dumaguete city). If the weather allows, many resorts are also doing day trips to Siquijor and Sumilon, which gives you even more variety.
Like the others mentioned, the weather is slightly unpredictable at that time. It can be absolutely stunning full on sunshine for days but since it's the typhoon season, we might get some afternoon rain showers too. Dumaguete is located so south that we usually don't get properly hit by typhoons, however, when the tropical storms go past the country the edges of the storm often brings rain for a couple of days. During the storm the weather might also affect on flights and ferries, so I would recommend sparing some extra time to reach your international flight and making sure you don't have too risky schedule on your departure day, where ever you are planning to stay and dive.
Happy holiday planning!