How common is the use of whipple shields or of any micro-meteor and debris shields in general for satellites in low earth orbit , I couldn't find any relevant statistics on the internet, a rough estimate would suffice.
MLI is a good example, used widely for the primary use for thermal control but has properties for a whipple shield.
Looking a little further will pay off: https://en.wikipedia.org/wiki/Whipple_shield cites
"There are over 100 shield configurations on the International Space Station alone, with higher-risk areas having better shielding."
and in turn leads to this reference https://web.archive.org/web/20130225001045/http://ston.jsc.nasa.gov/collections/TRS/_techrep/TP-2003-210788.pdf which has plenty of examples with ballistic limit equations for examples of MLI and other types of shield used on the ISS.
In addition to @Puffin's answer, it is becoming increasingly common for satellites to opt for dual-purpose design, where various structural and other elements serve as shielding for vulnerable components. This is as simple as making sure structural shear panels can protect propellant tanks, radiators can protect wiring harnesses, etc.
To a degree, I would say it's reasonable to assume that just about every modern satellite in LEO has some degree of shielding, whether or not it's dedicated shielding that wouldn't otherwise be there if not for MMOD.