The spanner DOES become useful if the component is missing less than 40 HP
So
that's the reason why...
In my entire career as an Engineer, you would not believe how many times that has happened to me, when the hull is teetering on the edge of being junked and unjunked and I have kept it alive, using just the spanner. I remember when I first had this happen to me, it was like my second game.
So, alright. Let's just settle this right here:
I will admit now (after a little testing of my own), that the mallet does have its perks mid battle.
Where are you getting this idea that your teammate is not helping you by whacking a near-death component with a mallet, or that your spanner is managing to provide more uptime or less direct hull damage when it's constantly near death? Are you talking about a Squid or Spire, with notoriously fragile hulls?
The first time this happened was on a Pyramidion I was flying with my friends, second game we ever played. We were under direct enemy fire and I was, I admit, panicking as our Hull Armor started to drop and our Hull Health was about 10%. I was beating on it with my spanner repeatedly, somehow keeping its health up as we were hit with Flak. I told my friend, a fellow Engineer, to get the engines while I get the hull. We were still getting shot when, after finishing the repair work on the engines, hit the hull with his mallet. My first reaction was "Oh good, now I can stop nursing this thing" and within a few seconds after that initial mallet strike, our armor was gone and we didn't have time to repair it before we blew up.
Since then, I've had this happen to me on six separate occasions on (mostly on Junkers, Pyramidions, and yes, the Squid), most of which resulted us in losing the game.
It's weird, mate.