You seem to be confused about vocabulary. \@numbers takes a reference to @numbers, which is the opposite of “dereferencing“.

It is needed because the natural representation for a matrix is an array of arrays. Since a perl array can only hold scalar values, arrays of arrays are actually arrays of references to arrays. PerlLoL goes into a lot more detail about this concept.

Without the backslash, all numbers would be squashed together inside @matrix without structure. The result would effectively be a list, not a matrix.

The question about split is easy to answer by looking at the doc. Without any argument, split splits $_ on whitespace. It is equivalent to split /\s+/, except that leading whitespace in $_ is ignored.