For example, if I say "Supposons qu'il y ait [qch], cela signifie que ...", where "cela" refers to the "[qch]", then should I use the subjunctive of "signifier"?
No, you don't use the subjunctive for signifie.
"Cela signifie..." is a main clause. You could change the comma in your sentence for a full stop:
Supposons (main clause 1) qu'il y ait [qch] (subordinate clause). Cela signifie (main clause 2) que [...]
Most of the time, subjunctive occurs in a subordinate clause, not a main clause. You could however use conditional (cela signifierait que) to mark hypothesis.