These issues translate to digital node-based systems- dealing with structured data in e.g. Max or TouchDesigner becomes an exercise in patience, and their mechanisms for composing and reusing code are somewhat baroque as well.
The other major creative limitation of flow-based programming (and in fact, most computational art systems) is the absence of a timeline (as mentioned by another commenter). This is a showstopper for many creative pros Ive talked to. But it grazes on topics that are interesting purely from a computer science perspective- imagine if you could freely jump to any point in a program's execution?
To be clear, having spent my doctoral studies in this space I find these to be interesting problems to solve rather than indictments of node-based programming as a whole. Im interested to see how eternal and other efforts mentioned in the comments here tackle these and other challenges.