Even if it's labled, diferent software interperets the labels diferently. GeoServer for instance when dealing with the WMS protocol, interperets 'EPSG:4326' diferently depending on which version of WMS you are using. 1.0 goes one way, 1.1 or 1.3 the other. At one time it may be serving a 1.3 WMS by merging layers from remote 1.0 and 1.1 WMSes, and has to keep track of which way to flip things for each data set, even though they may be labeled the same.

The original WMS spec didn't specify an order. Lots of programmers assumed lon/lat, but the geographers at the standards body wanted lat/lon, and 'clarified' it by declaring that the correct order years later.