I'm traying to use the R package "nondetects" to impute Ct values for the non-detects I have obtained on my RT-qPCR results. Is there a minimum number of genes I should have in my qPCR to provide enough data so than this R package is able to replace non-detects with
an imputed Ct value? Is this package just applied when you have a large scale analyses such as microarray?

You need to have enough genes (and samples) to get a decent estimate of the missing data mechanism. This package is designed for qPCR data (not microarrays). The 3 example data sets included with the package should provide a sense of the size / type of data sets that can be used.