should I open a solder mask over a high speed microstrip line in a PCB?
1.3GHz rectangular pulses.... is this actually digital data?  If it is and the clock frequency is 1.3GHz then the actual frequency of the signal is 650MHz and I would recommend the frequency of concern to be 3rd harmonic which is 1950MHz.  At this kind of frequency I would just make sure that you account for the effect of the soldermask in your impedance calculations and leave it.

If you actually have rectangular pulses of analog data and the frequency is 1.3GHz then I would try to preserve 5th harmonic of 6.5GHz, which is getting to a frequency where things really matter.  In this case I would say maybe microstrip isn't the best structure and consider stripline.  If you HAVE to use microstrip then do some simulation for the length of your line with and without the soldermask (and with the line geometry adjust for the presence or absence of the soldermask) and decide what you can live with.  If you can't simulate then base the presence or absence of soldermask on the line length.  For long lines (greater than a several inches) consider soldermask removal (although you may find that the nickel in ENIG, if that is your plating, is worse than soldermask would be).  For shorter lines the soldermask is fine.

A couple of other things... how long is this microstrip?  less than an inch... less than several inches ... more than 30 inches?
I have boards with over 70 inches of microstrip with frequency content of 15GHz.  I remove soldermask, and do tin plating.  The nickel in ENIG (and, obviously, any other plating with a nickel barrier) causes significant high frequency loss over these long lengths.  I have plenty of other designs at similar frequencies but with line lengths less than 3 inches where the soldermask and even mask over ENIG have perfectly good signal integrity (as long as geometry is correct for the presence of mask).