- Large programs / graphs? I can browse maps and photos of the entire planet from my web browser. ZUIs are well understood now. Also, computers got really big and fast. My graphics card has 8 GB (!) of RAM. Find a VPL that was designed for the era where graphics are cheap.
- Automatic layout is hard? Yes, an optimal solution to graph layout is NP-complete, but so is register allocation, and my compiler still works (and that isn't even its bottleneck). There's plenty of cheap approximations that are 99% as good.
- No formal spec? They sound desperate to come up with excuses why something can't work. How many (textual) programming languages had a formal spec before they got popular? I tried to look up when Ruby got a formal BNF grammar, for comparison, and it seems the answer in 2020 is still "nope, whatever parse.y does (13,000+ lines of C), that's Ruby".
- Difficulty to create editors? This is a legitimate concern, as it's true "there are no general purpose Visual Language editors", but that's an economic issue, not a technical one. Plain text is one of the very few formats where we have general-purpose editors. In most areas of computing, profitability has taken over, and companies refuse to cooperate. There's no one word processing or spreadsheet or database format, either.
- Lack of evidence? Again, they're holding VPLs to a higher standard. When a language like Ruby appeared, nobody asked for proof. Simply creating something that some programmers liked was sufficient.
- Poor representation? That's an issue with all kinds of programs! If I had a nickel for every horribly written program I've had to deal with in my life...
- Lack of portability? This is another symptom of the editor problem, above. Make a standard file format, and actually figure out how to get people to use it, and there's no problem.
These issues are from an article written in the 1980's. The same day as its publication, Apple released the Macintosh IIci, with a 40 or 80 MB hard disk, 1 or 4 MB of RAM, and a 640x480 pixel display. (For all that computing power, the starting price was $6269 -- only slightly less than the $6615 starting price for a Honda Civic that year.) Clearly, visual programming was a non-starter in that day and age. So were 90% of the other things I do on my computer every day. That doesn't mean they're bad ideas.
If you'd have asked me to write down a list of issues with C++ in 1989, I'd have a list that was similarly useless in 2020.