It's more or less accurate to say that our submarine commanders did not like or want to operate in shallow waters. These boats were certainly never designed nor intended to operate in the Java Sea...but, much of their operations were in adjacent waters that were quite a good deal deeper (as off Makassar Str. where depths were reported as in the 45-140 fathom range, they thought).
And there are surely instances in which the boats exceeded their designed limits in order to evade Japanese ASW units.
One rather typical order from ComSubs AF could say 'Operate off such-and-such island and "confining operations to a 30 mile radius and to keep in deep water" '--
A number of entries in patrol cruise books record depths of 60-110 ft when on patrol, coming up every 15-20 mins for periscope observations. One such patrol records running at 55 ft along the 100-fathom curve (somewhere near an entrance to Makassar Strait, apparently.)
At a glance, the deepest water I see for this particular S-boat patrol (early February 1942) was 180-204 ft and that in order to evade multiple direct depth-charging attacks after sinking or damaging a Japanese destroyer, I believe.