We can't fully answer that question as it would depend on the usage of the farm and your custom .NET application. However, it is non-optimal. SQL hosting SharePoint databases requires MAXDOP of 1 which eliminates parallelization of queries. In addition, you're introducing additional memory pressure.
Deploying a secondary non-SharePoint web site also has the potential to impact SharePoint performance, but more importantly security. I would be concerned about a custom developed web site being deployed to the same server hosting SharePoint.
With all that said, you can absolutely do it, but think about the potential performance and security impact.