If you do add column types to your tables as in traditional databases, then of course you should expect some varying behavior based on that.
I can imagine some potential for issues from people expecting to insert exact decimal numbers and choosing floating-point by accident, perhaps, or using integer types for actually-text numeric ID fields. If you go all-strings on input with no column affinity, then you'll get the same strings on output, though, so that's isomorphic to good-CSV.
¹ https://www.sqlite.org/datatype3.html – §3.1 “If the declared type for a column contains the string "BLOB" or if no type is specified then the column has affinity BLOB.” + §3 “A column with affinity BLOB does not prefer one storage class over another and no attempt is made to coerce data from one storage class into another.”