Many published single-cell RNA-seq experiments do not have replicates even in high impact journals. This is obviously less than ideal, but it seems to be an accepted practice. Is there a justification for that (possibly with a reference)?
I think the main justification so far has been that you have thousands of replicates, if you will (i.e., every cell may be a replicate of another one).
I'm not saying I'm fully buying into that argument, but the questions of replicates can be frustrating to tackle even at the bulk RNA-seq level, but trying to come up with a sensible answer for scRNA-seq is even less straight-forward. I guess it might also depend on the type of question you're asking. For example, if you want to find a new cell type, then by all means, do your scRNA-seq sequencing, find your cell type -- and then you will have to prove its existence in many other types of experiments anyway, e.g. via antibody-based analyses, FACS sorting and so on.
For what types of analyses does the lack of replicates worry you?