I have the main wordpress installation (domain.com) and the second installation in the subfolder (domain.com/eshop) . Is it possible to set the logo hyperlink from second installation to the main installation home page?
No there is no option. Two different installations are two different domains. Clicking this logo domain.com/eshop you will get on homepage of domain.com/eshop and the same for domain.com. This is the default functionality of WordPress it will work in such a way on any theme.
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