I have weighed the Java naval base option and have come to a conclusion. In my opinion, the naval bases in Malaya, Philippines, Hong Kong, and the Caroline Islands have all of the range you need, that a base in Java would provide. You can see this for yourself by moving 3 sea zones away from Java in any direction, and see that the naval bases listed above can reach. Any operation that you may be considering in the Indian Ocean can be reached by the Malaysian naval base.
Now moving forward with “new strategies” being conducted from a naval base in this location, I have come across a few that are feasible for the Japanese navy. During WWII there was an operation called “Divine Dragon Operation No.2” in which the Japanese used submarines to attack allied forces staged near Madagascar. You can tweak this real life scenario to fit your Japanese strategy in the Indian Ocean in a few different ways, that can be effective.
First the Japanese can send submarines, to the eastern coast of Africa, effectively disrupting the convoy of three sea zones (71, 72, 80). This can disrupt a total of 12 IPC’s depending on the neutrality of some of the nations, but more realistically you can disrupt about 6 IPC’s a turn from the UK. Your 3 Japanese subs will cost only cost you 6 IPC’s because you already start the game with 2, and the likeliness of the UK being able to destroy these submarines will be low considering the first few rounds of the game will prove costly for the UK fleet. That being said, it is not of much strategic value to the Japanese to do this, unless you are assisting the Italians to take control of Africa. By diverting the UK, you open the door for Italy to make moves in northern Africa.
The second strategy that I find more reliable for he Japanese, is to take South Africa at the beginning of J4. This would be possible, using landing forces, along with a few carriers. The UK would never see it coming until it was too late. At the end of J3 you can have an invasion force staged in SZ 75. The value is actually pretty great here. Japan although it does not have a bonus for doing so, would have about 10 IPC’s within just a few turns, cutting those IPC’s from the allies and mainly the UK. It also cuts any support from South Africa for the UK, making it easier for the Italian forces to take control of northern Africa. Alot of people will argue that this is a waste of Japanese naval forces, however by the beginning of turn 5, the Japanese can move their navy right back to the coast of West India, with an invasion force to assist in an attack on Calcutta on J6. Now this does leave your backside open for the US to move into northern waters, however with the appropriate defensive purchases, they should not be able to hold anything for a turn, leaving Japan in control of mainland, as well as having a strategic foothold in Africa.
Now all of that being said, the additional naval base in Java is not necessary if you use the Malaysian naval base. This strategy has not been used very much at all, so I cannot give advise as to whether or not it is tried and true, I have considered this before, and do plan to implement it at some point. The Japanese navy did at one point consider taking Madagascar and a forwarding base, to destroy supply lines and communication for the allies in the Indian Ocean and East Africa, however the Admirals did not find it strategically necessary because they felt that the Allies could retaliate and destroy any Japanese forces in that area, because of weakened supply lines for the Japanese considering the distance.