Since WhatPulse 2.8.2, you can pick from 2 tray icon colors. A black or white scheme. The client tries to detect which color will fit best to your window environment (if it's light or dark), but it might disappoint and pick the wrong color.
So if you have a dark theme and the icon is black, here's how to change it. Open up the Settings and change the "Client logo color" from "Auto" to either "Black" or "White":