The larger the entrance aperture, the greater the light-collecting capability. Now, you didn't specify that, but that does matter in your final choice.
Next, as the comments suggest, the choice of optics depends on the cost vs. quality trades. You want not only a given magnification but also as little coma, distortion, spherical aberration, and so on. At a very simple (and probably unrealistic) level, the longer lens pair (1000,20) might be easier to fabricate with low aberrations. In real life, we quickly descend into multi-element systems, or cemented doublet designs, and so on.
I'm guessing you are talking about a Keplerian design (two positive lenses), in which case consider how much longer the physical telescope is in the 1000-20 case.