This is a tough issue. First of all, it's likely that your tubing fittings are not "qualified components" under the B31 Codes. Second, the fatigue loads that are applied to hydraulic and pneumatic power systems are a result of pressure cycles and fluid acceleration and deceleration forces. Most such piping systems see only minor temperature variations during their usual operating cycles.
All this leads to the conclusion that the B31 Codes are not terribly well suited to the analysis of such piping. Neither B31.1 nor B31.3 claim jusisdiction over such piping; B31.1 specifically excludes the drops from the headers to the tools or machines in 100.1.3 (C).
nothing else is better, though. For detailed analysis of a small portion of the system, FEA would be a good tool, but it's clearly not warranted for a whole piping system. And the enclosed volume would be way to small to fall under the jurisdiction of the BPVC, even if you tried to include it. There are other Codes that apply to hydraulic piping systems. You might want to read this for further enlightenment (?).
http://www.wbdg.org/ccb/DOD/UFGS/UFGS%2041%2024%2026.pdfI would strongly argue that the wall thickness calculations should be done under the rules of B31.3 and after that it's up to the designer. If you are concerned with the margin of safety on wall thickness, you may want to model the system and apply the pressure cycle and fluid transient load cycle to the system. You will then have to go back and do a hand calculation using the methodology of 302.3.5 to determine the "equivalent number of cycles" for the piping system. You could use this to make a good guess at the minimum fatigue life to expect for the system, but it would be little more than that; a statement of the 95% confidence level of the fatigue life of the system. That's pretty good, but one man's 95% confidence level is another man's guess.