Reference samples are commonly used for the calibration and quantification of nanoscale electrical measurements of capacitances and dielectric constants in scanning microwave microscopy (SMM) and similar techniques. However, the traceability of these calibration samples is not established. In this work, we present a detailed investigation of most possible error sources that affect the uncertainty of capacitance measurements on the reference calibration samples. We establish a comprehensive uncertainty budget leading to a combined uncertainty of 3% in relative value (uncertainty given at one standard deviation) for capacitances ranging from 0.2 fF to 10 fF. This uncertainty level can be achieved even with the use of unshielded probes. We show that the weights of uncertainty sources vary with the values and dimensions of measured capacitances. Our work offers improvements on the classical calibration methods known in SMM and suggests possible new designs of reference standards for capacitance and dielectric traceable measurements. Experimental measurements are supported by numerical calculations of capacitances to reveal further paths for even higher improvements.