Interpreting SNP-in-gene associations from GWAS studies
In short, yes. 

If a gwas study links a SNP to a particular phenotype then yes, it is an effect of a single copy. Bear in mind, however, that a SNP is not a knockout or even a knockdown. It can be, but it is not always the case.  SNPs can produce a change in the protein sequence or in the regulation of the production of that protein. Both types of variation can result in a phenotypical change.

In any case, SNP information is always about a single allele, I imagine that you can find cases where a cell is homozygous for a particular SNP but is is not necessarily, or even often as far as I know, the case.