I recently flew over Netherlands with a mode a/c (not s) transponder. You may not turn it on in Dutch airspace. More to the point you may not fly above 1200'. With a mode s transponder switched off (as required under TMA) you can fly higher!!!!!!!!
Bit off-topic but you can't go higher there. From 1200' to 1500' you're in the SRZ Schiphol which is not allowed unless you have PPR (which is only given if you've got a good reason) and from 1500' upwards you're in the Schiphol TMA which is class A.
Outside the lateral limits of the Schiphol TMA / SRZ Schiphol you can go above 1200' with a working mode-S transponder only, according to the rules, but it's relatively easy to get a waiver for a transit through the Netherlands with just a mode A/C transponder.