SQL Server 2005 still running after in place upgrade to sql 2012
Any uninstall of SQL Server will not delete the data or log directories used by the particular version.

The reason your data and log files stayed in the same spot is because you did an inplace upgrade. It will not move the databases to the "new" folders SQL Server 2012 would create (eg. "..\MSSQL11.MSSQLSERVER\DATA").

The only issue you could hit when removing SQL Server is with the shared tools (e.g. SSMS, etc.), but since 2012 changed to using full VS it should not cause any issues.