This one really troubles me. I guess it's because I've seen too many CAD files with data all on one layer, differentiated only by color.
What it comes down to is really a choice between organizing the data by structure, or by attribute.
Given that choice, I would always go for organizing my data through data structure.
For a start, when processing data you have one less hoop to jump through (eg select a,b,c from table where id=X as opposed to select a,b,c from table where id=X AND lid = Y)
Then, consider why databases allow multiple tables - if a data format offers particular data structures you have to think they will process data more efficiently if you use them.
But the big issue (for me) is when you want to move the data out and into another system. Then I think it becomes a real challenge, because the end application might not use data in the same way. I've seen so many people come unstuck in this scenario.
So - in my experience - you'll be able to use and transfer data twice as efficiently when it has a decent (deeper and more structured) data model.