1. I think yes even it doesn't affect on phenotype but can affect genetic map

2. Surely yes

1. a genetic marker (without any functional effect on phenotype) is considered as a good marker if it is in linkage disequilibrium with several (many) polymorphisms/DNA mutations....some of them may be involved in a particular phenotype.

2. If a polymorphism is fonctional and could affect some phenotypes, it can be used in a genome wide association study; if there is an association between this polymorphism and a phenotype, this polymorphism may be causal. Also, such polymorphisms can be used.

I agree with @Pascal Rihet