hex format

For example, R already provides both hsv() and rgb() to create colours
from vectors of three numbers, but the correspondence is different in each
case.

Sorry if some consider this off topic:
HSV as a color space is really only liked by computer scientists.  Image
processing and color engineers rarely if ever use HSV.

There are MANY other color spaces and computations possible (see "color
spaces" or "color conversions" or other color topics on  this page
http://www.efg2.com/Lab/Library/Color/Science.htm).  Most of these color
manipulations in R are not easy because the very first step, converting
colors, I mean numbers <g>, like #ff0080 to the red, green components is
hindered because one must reinvent the wheel of hex-to-decimal conversion.

Yes, and convertColor in R-devel does quite a few of these (XYZ 
tristimulus space; CIE Lab and Luv; sRGB, Apple RGB and roll-your-own 
RGB based on chromaticities of the primaries; and chromatic adaptation for 
changing the white point).  The "colorspace" package has a more elegant 
implementation of a somewhat different set of color space computations, 
and R-devel also has hcl() for specifying colors based on hue, chroma, and 
luminance (polar coordinates in Luv space).

Basing R graphics on these (and so making them colours rather than just 
data about colours) requires a further step of considering the 
characteristics of the output device. This might be as simple as declaring 
R's output to be sRGB or as complicated as worrying about ICC profiles.

 	-thomas