Is there any non-aesthetic downside to salvaging everything in a settlement?

In Fallout 4, when first reaching Sanctuary after exiting the vault, I immediately scrapped everything (well, after looting the safes). Later, it got me thinking - maybe the contents of the safes re-spawn over time or something.

Disregarding that the area looks very empty and flat, is there any game play-related downside to clearing everything out?

The contents of containers do not respawn over time. Once you've emptied them they're empty and remain that way. This is different outside of settlements where entire regions will respawn (including enemies and containers). There is no downside to scrapping everything at a settlement.

There is a bonus to scrapping everything you can scrap in a settlement in that it increases the amount of custom objects you're able to build by essentially reducing the number of objects already at the settlement (since you're scrapping them).