I don't understand the question about empty values. A row with there empty values is just:

,,

And yeah, dealing with separators is annoying, but pretty much every reader supports quoted values and escapes (not every writer cares up add them, though).

In practice I use csv to process large amount of tabular data (like logs, events, etc) where I care about greppability and performance more than about potential for 0.001% of corrupted data. YMMV of course, if getting it 100% right is important use something else (JSON is not without sins too, consider that JSON numbers are often parsed as floats).