Hi @mikki,
Typically singletons are removed as a quality filter step, on the assumption that these may be off target hits (e.g., host sequence) or other errors/contamination that made its way into the sample prior to sequencing. If you're not interested in this quality filter, you could leave this out, or you could run with and without singleton removal and compare the results. Have you looked into the singletons to see what they are? You could get a rough idea of this using the qiime feature-table summarize and qiime feature-table tabulate-seqs visualizer. summarize can help you identify the feature ids of singletons (see the Feature Detail tab), and then tabulate-seqs lets you easily BLAST those against the NCBI nr database. Spot checking some of your singletons might give you a better idea of whether these are features you want to retain or discard.
I'm not an expert on DEICODE, so it may also help to have @cmartino weigh in. @cmartino, do you have input on this?