Hi there,
I know it can be considered naive but I am trying to plot normalised counts on selected genes, outputted from my deseq2, that I have further confirmed with rt-qpcr experiments (the idea is just to confirm that these genes follow the same, expected, trend).

since these genes are supposed to be significantly regulated upon my treatment, I was wondering if a statistical test should be performed on those or this should be considered as 'wrong step' to do.
How are you plotting the counts? Side by side with treated vs untreated? If so, why not just use the p-value from DESeq2? If not, you need to clarify what/how exactly you're plotting.