Just in case anyone else has the same question: In testing, I made a test copy of my world, then in the copy, used MCEdit Unified to select areas away from all bases, then set these unprotected chunks to repopulate. I am only selecting chunks with water, leaving most land biomes unchanged (selecting ocean, beach, and river). This left built-up areas unchanged but did spawn new biomes in all repopulated chunks, including ocean ravines, ruins, and shipwrecks. I didn't expect "repopulate" to actually regenerate terrain, but it did - quite noticeably showing the difference between 1.13 and prior versions near our main base, as a chunk adjacent to a protected section went from ocean to island. Have not done this to the live server world yet, working on the test copy only, with intent to copy to the server when 1.13 is stable in Spigot. (Will obviously keep an unaltered backup just in case!)
Testing showed that villages selected to repopulate respawned as expected, as did jungle temples. A newly created 1.13 world using the same seed as my original world generated shipwrecks and ruins in the same locations as in the repopulated chunks of my test copy, so (as with prior structures) these are not randomly placed. And replanting kelp/seeding ocean grass is a bit tedious but can be used to mask hard transitions between repopulated and "original" areas. Last, while Nether and End were not affected (as expected), Nether portals to repopulated chunks did work, creating a new above-ground portal in the newly-generated territory. Most areas were recognizable as the same from the original world, with mostly minor differences in terrain and shoreline.
If taking this approach be aware that any blocks previously placed or mined are reset when the chunk repopulates. For extensive mines you wish to save, you'll need to ensure that protected chunks include the underground areas you want to keep. This can result in some pretty big "empty" areas of ocean above.
If you aren't that worried about large areas, it might be way faster to simply prune those chunks rather than hand-editing the water-only bits. There is an MCEdit script floating around Reddit that automates the process by deleting all water or beach chunks, but I was too concerned about very specific (and widely scattered) shoreline bases to trust the full-auto approach. A bit surprised to see that repopulating and deleting were in effect doing the exact same thing - unclear if this is expected or not; perhaps the 1.13 update conversion process treats unpopulated chunks as if they need to be fully created from scratch.
End result: The important parts of the world are safe, the lightly explored or all-water areas are updated, and fancy new ocean features abound. I expect to see occasional awkward transitions due to the change in terrain calculations but I can live with it!