> Many graph problems also end up having lower bounds, being subject to conjectures like SETH or 3sum
Those are lower bounds on worst case instances. Not lower bounds on solving typical, practical instances.
> If you consider NP as second-order queries where the second-order quantifiers are only existantials, That will help explain why heuristics (educated guesses) help.
> A graph data type wouldn't have those heuristics.
Sounds like your heuristic for why heuristics help with many NP problems is less than helpful here.
In practice, you can encode many graph problems as eg SAT or integer programming or SMT etc and get good performance.
Even biggish instances of eg the traveling salesman problem are often solved well in practice.
I'm not sure why you bring up primitive recursive functions? Primitive recursion is able to express all of NP (and much more), so it's not much of a constraint in this discussion? (I agree that you have to try hard in practice to go beyond primitive recursion but stay finite.)