The cosmological potential of large-scale structure observations for cosmology have been extensively discussed in the litterature. In particular, it has recently been shown how Sunyaev-Zeldovich (SZ) cluster surveys can be used to constrain dark energy parameters. In this paper, we study whether selection and systematics effects will limit future wide-field SZ surveys from achieving their cosmological potential. For this purpose, we use a sky simulation and an SZ-cluster detection software presented in Pires et al. (2005), using the future Olimpo, APEX and Planck surveys as a concrete examples. We show that the SZ-cluster selection function and contamination of SZ-cluster catalogues are more complex than is usually assumed. In particular, the simulated field-to-field detected cluster counts is a factor 3 larger than the expected Poisson fluctuations. We also study the impact of missing redshift information and of the uncertainty of the scaling relations for low mass clusters. We quantify, through hypothesis tests, how near-future SZ experiments can be used to discriminate between different structure formation models. Using a maximum likelihood approach, we then study the impact of these systematics on the joint measurement of cosmological models and of cluster scaling relations.