Pipe wrench and spanner on a squid is a phase a lot of people go through until they realize how to engineer squid properly. You have to move around the ship constantly and pipe wrench hp repair is too low to help you with repairing anything, with light engines having 300hp, armor having 230hp, balloon having 1200hp and light guns having 200hp you can never fully repair anything on a squid with a pipe wrench that heals 120hp.
If you are moving around the ship all the time and your repair rotation because of that is about 7-8 seconds and sometimes more, you might as well have a mallet that can give you more repair for that time - doesn't matter if you have to watch a component finishing cooldown for a second or two afterwards.
When the engines die on the squid and you rebuild and then pipe wrench it, it doesn't even give you full hp engines in contrast to the mallet, which can save you a lot of hassle after hit by hwacha, balloon is obviously in need of a hammer and there is not even a question about that. The only arguable thing is the armor when you are shot by some heavy piercing stuff like a gat, in which some will say that the wasted hp after a mallet hit and the long cooldown is not worth it, I say that the lower hp repair is actually inferior because a lot of the times you are able to escape using the high speed of the squid so you can just mallet it quickly to get full HP instantly and run to the engines being burned to ensure full thrust, while with the pipe wrench the low hp repaired could mean you are stuck on the armor constantly rebuilding and repairing leaving the engines to the other engineer alone meaning you won't have them at optimal HP.
I like thinking of engineering on squids in three stages of thinking:
1. you think that having an engineer on the armor at all times camping it is the default position the engineer should be in, spanner-ing the armor 24/7 while the other engineer shots the side gun and repairs everything at the same time.
2. you no longer camp the hull and have the normal layout of one engineer on side gun and some engines with one engineer on armor and balloon and the remaining engines. But you think that mallet on the squid is bad.
3. you do the same as the second stage, only you use mallet and spanner instead of pipe wrench and spanner.
Also, mallet spanner buff is actually a pretty good loadout for certain ship loadouts that fight very specific ship loadouts as well. It's situational, doesn't mean it's bad.
But hey, all of the above is just my take on engineer loadouts and squids... No one is inclined to think the same.