Self-affine rough interfaces are ubiquitous in experimental systems, and display characteristic scaling properties as a signature of the nature of disorder in their supporting medium, i.e. of the statistical features of its heterogeneities. Different methods have been used to extract roughness information from such self-affine structures, and in particular their scaling exponents and associated prefactors. Notably, for an experimental characterization of roughness features, it is of paramount importance to properly assess sample-to-sample fluctuations of roughness parameters. Here, by performing scaling analysis based on displacement correlation functions in real and reciprocal space, we compute statistical properties of the roughness parameters. As an ideal, artifact-free reference case study and particularly targeting finite-size systems, we consider three cases of numerically simulated one-dimensional interfaces: (i) elastic lines under thermal fluctuations and free of disorder, (ii) directed polymers in equilibrium with a disordered energy landscape, and (iii) elastic lines in the critical depinning state when the external applied driving force equals the depinning force set by disorder. Our results show that sample-to-sample fluctuations are rather large when measuring the roughness exponent. These fluctuations are also relevant for roughness amplitudes. Therefore a minimum of independent interface realizations (at least a few tens in our numerical simulations) should be used to guarantee sufficient statistical averaging, an issue often overlooked in experimental reports.