Did the Wehrmacht consider these commando raids a threat? An annoyance?
Some raids had a major strategic impact: the raid on Saint-Nazaire, for example, put an important drydock on the French Atlantic coast out of action. Others were more regional in their impact, like the attack on the Glomfjord power plant in Norway. Others were pure showpieces, like the disastrous raid on Dieppe. You can debate the overall success or importance of the commando strategy, but they certainly had a psychological impact on German thinking.
A spate of raids in the spring and summer of 1942 — and particularly reports that commandos had executed captured German soldiers during the raids at Dieppe and Sark — infuriated Hitler sufficiently that he personally issued a 'no quarter' order that any commandos encountered by German forces were to be killed immediately, even if they were attempting to surrender. The 'Commando order' further mandated that any commandos who did end up alive in Wehrmacht custody were to be immediately placed in the custody of the Sicherheitsdienst, the SS intelligence service, and explicitly forbade their being treated as prisoners of war. Here's the crux of the order:
From now on all enemies on so-called commando missions in Europe or Africa challenged by German troops, even if they are to all appearances soldiers in uniform or demolition troops, whether armed or unarmed, in battle or in flight, are to be slaughtered to the last man. It does not make any difference whether they are landed from ships or aeroplanes for their actions, or whether they are dropped by parachute. Even if these individuals when found should apparently be prepared to give themselves up, as a matter of principle, no pardon is to be granted them. [...]
[...] If individual members of such commandos, such as agents, saboteurs, etc., fall into the hands of the military forces by some other means, through the police in occupied territories for instance, they are to be handed over immediately to the Security Service. Any imprisonment under military guard, in PW stockades for instance, etc., is strictly prohibited, even if this is only intended for a short time.
Essentially, the order recategorised commandos as spies and saboteurs, rather than soldiers. It was in direct contravention of the Third Geneva Convention (which dealt exclusively with the treatment of prisoners of war) — a fact not lost on the German high command, who went to extraordinary lengths to keep the order's existence secret. They were unsuccessful, and the order became a key plank in the later war crimes prosecutions of senior Wehrmacht officers: Oberkommando der Wehrmacht chief of operations Alfred Jodl was convicted and hanged at Nuremberg in large part because of his signing of the Commando order and the similar 'Commissar order', which applied to Soviet political officers. (See Volume XI of the IMT proceedings for documentary evidence and witness interviews used in the prosecutions.)
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