This is s a multipart answer due to the complexity of output possibilities:
Measuring within QGIS, distances should be Geodesic, (this will automatically be taking account of the changes in latitude longitude etc along the length of the line for you). In older systems and for long distances On Enroute charts etc the Great Circle distance is commonly reported. Remember that the longer the line the greater of margin for error.
In paper charts of 1:1,000,000 or less you can also use the geodesic distance (in system) if available, Cartographically you could measure distance from the scale bar, however more correct is to read the latitudinal scale and use that to measure distances within that latitudinal range especially north-south lines. Remember all measurements using distance from scalebars and latitudinal scale are approximations across the body of the chart.
Positional information should be calculated using calibrated tools with formulae that are known and verifiable. checking distances on a map plate with a projection and scale can be done as a ready reckoning crosscheck, but should not be relied upon to provide accurate coordinates to be read back into a system.
Calculated positions verified by the procedures designer should pass through the QMS and be verified and pushed back out to the cartographic system as data (AIXM for example).