Nanomechanical sensors based on detecting and tracking resonance frequency shifts are to be used in many applications. Various open- and closed-loop tracking schemes, all offering a trade-off between speed and precision, have been studied both theoretically and experimentally. In this work, we advocate the use of a frequency counter as a frequency shift monitor in conjunction with a self-sustaining oscillator (SSO) nanoelectromechanical system (NEMS) configuration. We derive a theoretical model for characterizing the speed and precision of frequency measurements with state-of-the-art frequency counters. Based on the understanding provided by this model, we introduce novel enhancements to frequency counters that result in a trade-off characteristics which is on a par with the other tracking schemes. We describe a low-cost field-programmable-gate array (FPGA) based implementation for the proposed frequency counter and use it with the SSO-NEMS device in order to study its frequency tracking performance. We compare the proposed approach with the phase-locked-loop based scheme both in theory and experimentally. Our results show that similar or better performance can be achieved at a substantially lower cost and improved ease-of-use. We obtain almost perfect correspondence between the theoretical model predictions and the experimental measurements.