?So what effect would this Stronger Netherlands have on Indonesia?
With close to twice as many citizens, I suspect Dutch colonization could be bigger, but I think the Netherlands will still focus on the colonies it has. Indonesia could be bigger and include Northern Borneo (but not Malaysia, as Malacca had been traded away before the Belgian revolt). Perhaps Eastern New Guinea will be included and the Solomons. Besides that I think (part of) Ghana could be Dutch, as the Netherlands still had some outposts there and perhaps some Pacific islands.
?Effect in any Great War between Germany/France?
?Effect on GW 2 v Japan?
The Netherlands could get involved in a war between Germany and France the same way Belgium did, but German-Dutch relations were always better than Belgian-German relations, so I am not so certain it would happen. Germany could try to convince the Netherlands to join them in an attack on France for the Dunkirk region (and maybe Lille, French Hainaut and Artois, traditional Dutch regions now in France), but the Netherlands didn't join the first world war for Flanders, so why would they join a war for those regions. I suspect the Netherlands will try to remain neutral.
The same could happen from France, France asking the Netherlands to enter the war against Germany for East-Frisia, Cleves and other German-Dutch border region, but I see no reason for the Dutch to accept as they never really were Dutch (except east-Frisia for a couple of years during the kingdom of Holland).
But as said, Germany (or France) could attack a neutral Netherlands, like Germany did OTL with Belgium. In that case the Netherlands will fight and retreat behind the waterline (which could have been extended to include Antwerp and the eastern part of Flanders. They will fight from their with whatever allies they have. The waterline will be a formidable defense barrier in the age before an airforce or paratroopers, certainly if it won't freeze over during winter (and even during winter I think it can be relatively easy defended by machineguns and artillery).
A war between the Netherlands and Japan? With a POD around the early 19th century the possibility could be butterflied away. If it isn't, the Netherlands and Japan were very friendly during the 16, 17th and early 18th century, so an alliance could be as likely as enimity. If it came to a war, the Dutch fleet will be stronger as OTL. Would they be able to beat the Japanese? Well it all depends on the butterflies. Is the Netherlands occupied during the war, what allies does the Netherlands have, etc.