I'd use:

$HoA{$key} = \@fields;
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unless I really wanted to copy the elements in @fields. Most often I'd do that sort of thing in a loop where @fields is local to the loop and the assignment is performed at the end of the loop block.

The trap with either of variants you show is that only a shallow copy is made. If @fields contains nested elements then the references are copied, not the nested data. Using \@fields makes it just a little clearer (at least to me) in that case that danger lurks under the surface because it is clearer that there isn't much copying going on.