Well, it happens that I work on railways so I know a bit about drainage as well. And you are right: for the relatively small investment, a lot can be improved. Drainage is "not sexy", so these projects don't get too much attention. Mostly it is reactive and only until something like that happens, it gets attention required, but then: most of the budgets are thrown on the responsive measures.
Having said that, it is worth to weight it if the money spent to mitigate 1 in 100 years event is worth it and I personally think that I am happy to give up the right to use underpass once in a long while if it means the money is spent elsewhere more efficiently.