I think that it would be unlikely that the Dutch navy would lay up the Java-class cruisers, or the older batch of Admiraalen-class destroyers. It is much more likely they would discard the old armoured ships and the obsolete G- and Z-class torpedoboats and the other scrap-iron still floating around in Dutch service. The cruisers and destroyers would still be valuable as convoy escorts for which there would be a great demand. They would probably have to be modernised though (Asdic on the destroyers and better AA armament for both).
Considering the relatively inexhaustible source of manpower represented by the East Indies, I don't think that a shortage of sailors would be the problem. There might be a shortage of officers of lower ranks after the lower ranks have been promoted to higher ranks due to the increase of the navy, but those places are more easily filled.
I think that after the outbreak of war the Netherlands would have started an emergency construction programme to build armed trawlers, ASW launches, like the B-class planned in the East Indies, and ASW frigates, perhaps along the lines of HNLMS van Kinsbergen. I also think (in a scenario where the Dutch neutrality is the only difference) that as good as all "heavy" units would have been sent to the Indies in 1941, since the Japanese aggression would surely have materialised on the same timeline. And I am pretty confident that the majority of these units would inevitably have been lost in the defence of the colony without making much of a difference.