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The best simulator for diagramming would be jbbs Bahn in my opinion. It is an horrible piece of software, no Gui to mention, you can't drive any trains and the graphics are from 1991. I have created the whole dutch network of 2003 in it though, timetabled and all. Including splitting and joining...
If you want to simulate any signalling you will need more than just the track diagrams. You would also need to know the shapes of the TC (track circuits) the used signals, overlaps etc etc.
You're best option is to go to Brussels and then change to the 'Benelux' the normal IC that runs between Brussels and Amsterdam. If you want you can go with the Thalys, but to my opinion the fee they ask (opposed to the flat fee for the 'any destination ticket') is way to high for the value...
That is the same for the dutch network (on both accounts) I can't think of many non-grade separated JNs, other then at stations (but even then, Rotterdam, Utrecht, Amsterdam and more all have multiple fly-overs).
In the Netherlands only few fly-overs were build before the 50sh. Admittedly...
It is not very uncommon to send locos around the country via passenger trains. this also happens in the Netherlands (although we do not have many passenger locos anymore).
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