The dynamical behaviour of wave energy conversion systems (WECs) can be described in terms of the well-known Navier-Stokes equations which, being significantly complex, preclude their use in control design and performance assessment procedures. As such, WEC devices are virtually always modelled in terms of rather simplistic dynamical representations, aiming to produce models which are tractable both from a computational, and an analytical perspective. These models, nonetheless, are inherently affected by uncertainty, introduced by the set of small motion assumptions used to derive such simplistic representations. Deriving methodologies for a sensible quantification of this uncertainty is hence fundamental to understanding the effect of these modelling assumptions in the overall control design and performance assessment procedures. This paper presents a set of experimental tests conducted on a prototype system, locked at different equilibrium positions to account for different wetted surfaces, with the objective of characterising the uncertainty introduced by assuming small device motion within WEC modelling. The corresponding modelling mismatch is quantified in the frequency-domain, and a family of WEC models is generated by means of additive uncertainty. Leveraging the identified set of systems, numerical simulations are performed to show the potential impact of this uncertainty in the performance estimation of this prototype WEC system, for different irregular sea states.