Thanks for bringing this up on meta so constructively.
The consensus here is that we use the term 'SQL Server' and not MSSQL - it might not always merit an edit just to make that change but it's always preferred.
Although the abbreviation MSSQL is often used, it tends to be by those who know the product less well - I just did a quick survey of blogs by household names in the SQL Server world and not one of them used MSSQL, rather 'SQL Server' was displayed prominently on their pages. As we want this site to be expert-led, that is a strong reason to prefer the term most used by experts in the field.
The issue of search is an interesting one. We are obviously not helping ourselves be found by those who use MSSQL to search. This is outweighed by the benefit to our reputation in using the more expert term. You could even argue that this reduced visibility to MSSQL searches is a benefit as it helps keep the site targeted.