You can stay in hotels that have places to lock bikes at night; ask to see the location before paying money. Usually, they are locked inside a locked area, and in the locked area you lock your bike.

You can buy food to take with you for lunches and snacks, reducing the need to worry about removing panniers from your bike. In smaller towns between Amsterdam and Brussels, you will likely be able to keep your eye on your bikes/panniers while you are inside eating. Or one of you can go inside the grocery to buy food while the other stands with the bikes. If you are credit card touring, you shouldn't all that much to carry, so taking the panniers off, if needed, should be a big deal, right?

We cycled to Gouda via Utrecht, then south to Kinderdijk, where there is a World Heritage site with windmills. Don't miss it. There's a ferry at Krimpen aan de Lek to cross the river to Kinderdijk. Just follow the signs. Can't help you after this; my friend crashed just after this, so we took the train to Brussels to rest her knee and then we rode out of Brussels.