NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely)
For a Complete genome it's fairly straightforward - if not present, a gene can safely assumed to be missing (or possibly present on plasmids, if those aren't available in the database).
But what about the others? With Contig-level genomes, I'd feel uncertain about making any statements (especially since some of these projects are split into thousands of contigs). But what about Scaffold, or Chromosome? Are they expected to be complete in terms of genes, but just missing repetitive sequences?