Is a paper with no citations likely to contribute to citation metrics in a way which reduces my job prospects?
No, this is not a problem. Everyone has papers on their CV which have few citations, including older papers. If this were true for all your papers, in particular even all of those which are several years old, this could be an issue - but this does not seem to be a problem at all in your case. (Note that the distribution of citations vs. papers is somewhat similar for everyone, reflected e.g. in the fact that there is a clear relation between the number of publications and the h-index.)
Moreover, if you really feel later on that a given paper does not represent you well, you can always omit it from your publication record - you are not obliged to list everything you ever published there, in particular if you feel it is not relevant.
So I would go with being a coauthor of the paper, if the others offer coauthorship to you, and you feel it is deserved.
Edit: To follow up on your updated title, a paper with a low number of citations will not have a negative effect on citation metrics: Typical metrics are either the total number of papers, the total number of citations, or (most importantly) the h-index, none of which gets worse if you add little-cited papers. The only indicator which would be affected is the number of citations per paper, but this is rarely used - and even then, a single little-cited paper will not have a big effect.
I probably don't have the best perspective, having been out of academia for a few years, but as far as I know, anyone who cares about citation metrics will be using a standard widely-inclusive data source (e.g. Google Scholar) to get their data. So as far as the metrics are concerned, it doesn't matter whether you put any given paper on your CV or not.
More generally, I think it's quite rare that it would actually hurt to put a paper on your CV. The only case I can think of where you would actively want to not be associated with a paper is if the paper was retracted for some reason having to do with academic fraud, or something similarly serious, and in that case leaving the paper off your CV isn't going to keep people from finding out about it. Having no or few citations certainly isn't a reason to not want to be associated with a paper. It's quite a normal situation, especially as an early-career researcher.