A Spatialite database is just a SQLite database loaded with Spatialite module extensions including tables, triggers, functions etc. It is therefore possible to access a Spatialite database using the SQLite .Net Wrapper from https://system.data.sqlite.org and with the Spatialite module extension library mod_spatialite-x.x.x from http://www.gaia-gis.it/gaia-sins/, otherwise the spatial functions will not be available to your C# code.
While the Spatialite database can be created using the SQLite wrapper and the Spatialite module extension, the newly created database lacks all the Spatialite tables, triggers etc. necessary for proper functioning of the Spatialite database. I would need to run some initialization SQL to create all the required Spatialite tables, triggers, etc. So instead, I found it more convenient to create a template Spatialite database with the Spatialite executable beforehand. Then in the C# program, just simple copy the template to create a new Spatialite database.
The following is an example C# code snippet illustrating creating a new Spatialite database from a pre-prepared template and making a SQL query reading some Spatialite geometry fields from the database.