This is a letter to the general community: please stop writing these scripts in perl and bash one liners. That one off script you thought would only be used once or twice at this nonprofit has been in continuous use for 12 years and every year a biologist or journalist runs your script having no idea how it actually works. Eventually the script breaks after 8 years and some poor college student interns there and has to figure out how perl works, what your spaghetti is doing and eventually is tasked with rewriting it in python as an intern project (true story).
I think your complaint isn't really about perl and bash. It's about knowing your audience.
When writing code that will be used by a particular sort of user base, the code should be written in whatever way best suits that user base. If your users are academics, researchers, journalists, etc. -- yes, avoid anything with complex or obscure semantics like perl or bash.
But if your code is going to be used by programmers or people who are already comfortable with perl/bash/whatever, those tools may be just the ticket.
He has a valid point, though. I've seen (and written!) one-liners that were so complex that nobody, even devs, can deal with them without decoding them first.
They aren't technically "spaghetti", but they are technically impenetrable.
I argue that one-liners like that aren't good for anybody, dev or otherwise.
