What does this information about "upper limit column densities" and "upper limit relative abundances" mean?
A column density is just the integral of a (number) density along the line of sight.

Often, you would get the same observational absorption or emission signature from a number density of $n$ molecules cm$^{-3}$, spread along a line of sight through a cloud of diameter $x$, as you would with a density of $0.1n$ spread over $10x$. 

In other words, all we can infer is the product or, more accurately, the integral of $n\ dx$, and this is known as the column density.

In the paper you refer to, I doubt they know the thickness of the shock they are investigating, so a column density is all that can be determined.

The relative abundance is more straighforward; it is just the ratio of the number densities of the two labelled species.