if I know the number of sequencing circles can I give this information to DESeq2?
You can include that info in the design, though you'd have to decide whether to include it as a number of just a factor.  I've never heard of anyone including PCR cycles.  I've heard of people including RIN scores, though I've never done it.
If the PCA looks alright, I wouldn't worry about.  I've got tons of examples of the lab people saying &quot;I did a few more cycles on these few samples&quot; and then you can't tell any difference in the PCA.  I think needing to do more cycles likely has more to do with variance in the prep than a real biological difference.