AS-That calculator has the OPTION of putting in a manufacturers' hub but does NOT require it. Simply skip it and enter the spoke count/cross pattern numbers in that part of the calculator. It will still do the calc.
IF the f&r hubs have a different flange diameter you cannot use the same length spoke with the same crossing pattern for both wheels. If you want TO BE SURE, simply take a little time to measure your hubs and rims. You have the hubs and rims in your hands and know where the tape begins and ends right? Very very accurate calculator. NEVER had a bad calc. Accurate measurements of your hubs and rims will bring good results. The trick in the end is the ERD measurement, or Effective Rim Diameter. Since the old wood rims are thick as AS mentions, the spoke goes waaaay into the rim through the thick wood in to the nipple shoulder/washer bed. This ERD is measured at where the nipple shoulder & washer seats inside the rim...
The Woodies are like around 1/2"-3/4" thick, unlike regular alu rims and a bit tougher to measure the ERD. The "correct" long, 3/4", two-flat nipple used on the thick wood rims only protrudes about 1/4" beyond the surface (hub side) of the rim. This ERD is the critical measurement. For these deep wood rims, I would suggest calculating the spoke length and then take 2mm off that number so the end of the spoke does not protrude past the nipple shoulder.
Or, you can trust Mr B above, invest in spokes and hope for the best. I would first confirm that his measurement is correct for a 4 cross 36 spoke rear wheel and check that his hub flange is the same diameter as yours. If maybe not then you are screwed. So again, use the calculator and it will save a huge amount of time and frustration. You just start with spoke number and cross pattern for each wheel before you start any spoke length calculation. Good luck!