For 16s and ITS2 rRNA gene sequencing the average number of reads per sample is close to 40-50K (pre-filtered). Most manuscripts tend to report pre-QC number of reads which will always be reduced after cleanup. The number of reads is driven by the number of multiplexed samples and the Miseq chemistry.
We recommend against over-sequencing as it inflates the number of spurious OTUs. The more reads that come out of the sequencer, the more likely those reads will create spurious OTUs.
We would generally not recommend omitting samples with low reads as there may be biological factors at play. Course-grained comparative analyses (e.g. beta diversity) are relatively robust to low reads.