The LM descent engine had this shelf lifetime problem only because they decided to store the pressurizing helium as a supercritical fluid to reduce mass. You can easily make such a system last indefinitely by just keeping the helium at ambient temperature, and that's exactly what's done on spacecraft that need to produce large delta-Vs after long periods of time, e.g., interplanetary spacecraft arriving at another planet.
The bigger problem is that the important hypergolic propellants freeze at fairly high temperatures. The main problem is N2O4, which freezes at -11.2 C. Straight hydrazine (N2H4) freezes at an even higher temperature, +2 C, which is a challenge for spacecraft that use it as a monopropellant. Bipropellant engines usually use a lower-freezing hydrazine like UDMH (-57 C) or MMH (-52 C), either pure or mixed with straight hydrazine (e.g., Aerozine-50, a 50-50 mix of UDMH and straight hydrazine). I don't know much about its low temperature properties but I've heard it will separate out and cause a problem.