Could you get exemption and fly higher or in controlled airspace with A or C XPDR if you ask ATC?
Officially, no. Unless you put a motivated request in writing, days in advance, yadayadayada. If you want to pursue this, start here:
Homepage - OPS help desk LVNL
In practice, what I've heard is that most controllers prefer that you use mode A/C instead of nothing if you don't have mode S. But it also depends on the airspace and altitude you're talking about, how busy it is, and the mood of the controller on that day.
Without mode-S, my primary plan would be to stay in class G below 1200' all the way, with the transponder turned off. You can then talk to ATC and see if they're willing to allow you higher and to use the transponder. But honestly, transiting Holland at 1000' is not an issue at all. In fact, lots of places where 1000' MSL is actually more than 1000' AGL...
Yes, as I recall pretty soon after they made everybody fit use mode S, they had to make all the VFR aircraft under the TMA turn them off again
Yep. Holland set the standard on how NOT to implement mode-S.
For those who don't recall the situation: Mode-S became mandatory somewhere in the middle of winter, so everybody had transponders fitted over the winter period. The first glorious day of spring, everybody decided to go flying - with their new mode-S transponder activated. This generated so many returns on the radar scopes, with so many data blocks associated with them, that the controllers simply could not distinguish their own traffic from the rest of the clutter anymore. This was particularly bad in the area around the PAM VOR, which is a choke point at low level for GA, but also a major waypoint for approaching and transiting IFR traffic.
So a NOTAM was hastily put together which essentially told everyone to turn their newly acquired transponder OFF in certain areas. That situation remained for, what, six months? That was the time it took for ATC to update their software and implement much better filtering options.
And still if Dutch Mil is doing maintenance on their radar systems and have to fall back to their backup sets, we are again being told to turn our transponders off in certain areas. Shame, really.
