Mainly performance but there are some issues with data management and migrations. But to put it bluntly it’s a nightmare to properly maintain a production MongoDB database (bias opinion I suppose, but I prefer to give it to you all straight).
To put it another way: Strapi is a strict schema, relational, headless CMS
MongoDB is neither strict schema, nor relational (and we don’t follow their best practices regarding child documents over multiple collections, effectively we treat it as a relational DB anyway)
SQL (PG/MDB/MSQL/SQLite) are all strict schema and relational databases. Strapi was practically designed around how SQL functions even if it wasn’t the first database we suggested. There is a reason SQLite became the quickstart option 
Source on MongoDB being a nightmare, I provide support, I look at any production MongoDB server and it gives me a headache. It will wake me up in the middle of the night with terrors 