It's good to hear about the practical challenges of keeping a digital lab notebook, although I think that many of them will also apply to keeping a well-organised paper notebook!

"anything but a very simple data model is likely to be fatally flawed when recording an experiment"
I totally agree. The question is what you want to do with the model of the experiment. Simply exchange a description of the experiment with other software? Or to get some machine to reason over it?
Is anyone working on a simple data model for an experiment? The only ones I'm aware of are complex Functional Genomics ones like MAGE-TAB.