It is by hour, and by job in most places, as they refer to the book for the number of hours. It is unlikely that you will get both tie rods replaced for the same labor charge you would get one replaced for.
If both tie rod ends are about the same age, then there is a decent chance that the other one will fail sooner rather than later as well.
While that doesn’t necessarily mean that you need to replace the second one right now, and you probably won’t really save a whole lot on the job as far as the labor goes by doing them both at once, there WILL be a savings.
After replacing a tie rod end, you need to have the front end realigned. Unfortunately, this is unavoidable. Most places around here get between $50 and $80 or so for front end alignments. Now, if you have just the bad end changed, then drop $50 for an alignment, then two months later the other end needs to be changed, while it won’t really cost you any more to get the other end changed two months from now, it WILL cost you another $50 to get it aligned again after the 2nd end is changed, so that is something to consider.
It is always difficult when you are on a tight budget to decide which route will cost you the least in the long run. I personally do tie rod ends myself, so I only pay for the alignment, and if one is bad, I go ahead and do both, because I am only paying for the parts.