Well, I seem to remember there's a Dutch requirement to have Mode S to fly above 1200ft AGL in controlled airspace.
Not quite true. It's mandatory to have a mode-S transponder above 1200ft (MSL) period. And it's mandatory to have mode-S in any kind of controlled airspace, at any altitude. In other words: The only time you don't need it is when operating in class G below 1200'.
On the other hand if you're just transiting Holland on your way to Scandinavia it's perfectly feasible and safe to do so at 1000' MSL, remaining outside controlled airspace all the way, so indeed it should not be a deal breaker.