As far as I know a single c4 doesn’t space the entire shuttle - it doesn’t make a hole in the floor, it can only take down walls, which can actually be fixed. Unlike the lattice of the evac shuttle, which, if destroyed, currently can not be fixed (which is the problem with minibomb use on the shuttle)
The evac shuttle should not be bomb proof, but they should be designed better to account for spacing. Right now there are multiple designs where people use RCDs to build firelocks in order to make the shuttle more resistance to spacing (I see engi borgs do this from time to time). This should just be standard shuttle design, if a wall is breached, it shouldn’t space the entire sitting area. Even if we ignore shuttle bombing, in universe this makes sense, its a shuttle, it’s not like there aren’t meteors or debris in the sector, it makes sense for it to be ready incase of a wall breach without needing an engineer to fix it.
Right now shuttles are also very weak to gas leaks - if someone gets a plasma can on the shuttle, they can open it and kill (even ash) a huge portion of the crew. I’m not 100% on that, but wouldn’t additional firelocks also help prevent that?