Bombadil's brooch

[Raynor]

I believe that the whole history of Numenor, Gondor and Arnor shows a huge respect for the burrial grounds.

Originally Posted by Letter #154

In their way the Men of Gondor were similar: a withering people whose only 'hallows' were their tombs.

Originally Posted by Letter #156

But in a kind of Noachian situation the small party of the Faithful in Numenor, under the leadership of Elendil, Isildur and Anarion ... established a kind of diminished memory of Numenor in Exile on the coasts of Middle-earth – inheriting ... the yearning for longevity, and the habit of embalming and the building of splendid tombs – their only 'hallows': or almost so.

Seeing that these lasting dunedain are called "faithful", I believe that they remain true to the core values of their kin.
Also, even if some tombs are not prone to floodings, that can be easily accomplished with some engineering efforts - cannals, small dams around the barrows or whatever. Also, I don't think that the orcs would have excluded the barrows from their suspicion list, seeing how they demonise their opponents. I found your refference to the barrows being closed constructions very interesting. From what I saw around the internet, it does seem that at least nowadays they are so, perhaps they were so from the begining, so as to avoid looting or profanation from animals.