Failure to put the head alignment dowels in will lead to side to side movement of the head and eventual head gasket failure. The head bolts are there to counteract the pressures that result from combustion. The holes in the head where the bolts go aren't machined to the tolerances that the head dowels are so movement is possible. The dowels are plenty strong enough to prevent side to side movement.
I'd always use them as PKRWUD already suggested.
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