Some pens left the factory with imprints made more prominent by being colored in. The nesting pelican logo on the cap top of Pelikan pens is one example; the orange-red infill of the model numbers stamped into the end of black hard rubber Watermans is another (on most colored hard rubber Watermans, the infill was silver instead). In most cases, however, imprints were left unfilled.
In recent years, however, the coloring-in of imprints has become popular among collectors, many operating under the mistaken belief that such imprints were the rule, rather than the exception. This practice appears to have taken off as a byproduct of the desire to make imprints more visible on photographs of pens displayed online. The most popular means of coloring imprints have been grease pencils (also known as china markers) and wax crayons. Although these coloring agents are not permanent, it can be rather tedious work to remove them entirely.
Personally, I don't much like colored-in imprints -- and only in part because the coloring is not true to the pen's original appearance. Coloring may allow a light imprint to be read more easily, but it also makes that imprint too bold and obtrusive. In fact, when photographing very faint imprints, infilling is not nearly as effective as careful use of raking light. And when photographing stronger imprints, raking light allows one to get a view of the whole imprint that shows its depth, strength, and degree of wear -- aspects that are largely obscured when an imprint is filled up with colored wax. For imprints are pressed into the surface of a pen or pencil, not screen-printed on top. They are three-dimensional, with a sculptural quality parallel to that of a hand-cut inscription on a stone monument. Fill them in, and the effect is very different, and much the poorer.
NOTE: A rare exception to the general rule about colored imprints would appear to be some Mandarin Yellow Parker Duofolds which left the factory with blackened imprints. Incontrovertible evidence for this comes from a mint and stickered pre-streamline era pen and pencil, where the original price bands partially covered the imprints, leaving no doubt that the coloring of the imprints was factory-original. Interestingly enough, however, the coloring agent was quite thinly applied, and did not fill up the recesses of the imprints as do the colored waxes favored by present-day collectors.