Nitride microcavities offer an exceptional platform for the investigation of light-matter interactions as well as the development of devices such as high efficiency light emitting diodes (LEDs) and low-threshold nanolasers. Microdisk geometries in particular are attractive for low-threshold lasing applications due to their ability to support high finesse whispering gallery modes (WGMs) and small modal volumes. In this article we review the effect of defects on the properties of nitride microdisk cavities fabricated using photoelectrochemical (PEC) etching of an InGaN sacrificial superlattice (SSL). Threading dislocations originating from either the original GaN pseudosubstrate are shown to hinder the undercutting of microdisk cavities during the photoelectric chemical (PEC) etching process resulting in whiskers of unetched material on the underside of microdisks. The unetched whiskers provide a pathway for light to escape, reducing microdisk Q-factor if located in the region occupied by the WGMs. Additionally, dislocations can affect the spectral stability of quantum dot emitters, thus hindering their effective integration in microdisk cavities. Though dislocations are clearly undesirable, the limiting factor on nitride microdisk Q-factor is expected to be internal absorption, indicating that the further optimisation of nitride microdisk cavities must incorporate both the elimination of dislocations and careful tailoring of the active region emission wavelength and background doping levels.