Lets first get the terminology right, LINQ is not exclusive to database querying. There is LINQ To Sql, Linq To Entities, etc. If one does not design the DBML correctly then indexes will not be used but that is not the developer writing the queries problem, its in fact the person who designed the table. The same can be applied in your situation (and it happened numerous times when i was there).
The fact is that in this day and age with all these compute clusters and with bigdata like _kabal_ said a lot of the heavy lifting can be loaded onto a clustered EC instance (2 Intel Xeon E5-2670 8-core processors, 244 GiB of RAM, 240 GB of SSD-based). With that type of power i don't need some puny database to do my "heavy work". And there are much more intelligent ways to write datawrappers/layers without the need for
C/R/U/D sprocs and other random ones.