It's a bit of a multi-level problem. Firstly, the design of the bearing retainer clip absolutely matters on the IS52/40 headsets. If you don't have a clip with a deep seat, a rough hit will cause the seat to rise out the groove and come loose. Remember, you've only got at best 270 degrees of engagement with the seat on a narrow 2-5mm 45 degree chamfer.
If the clip is a poor design, you can even split them as many road ones are thin aluminium, with cut outs to allow them to compress/spring into the bearing seat - these will act as stress raisers and be a point through which it cracks.
Finally (and this is generally not an issue), the headset cap may be composite or resin which could fracture in a crash, especially if you have a large force through the steerer tube. This is why most MTB headsets are metal, but again it is not always the case (depends on the intended use).
Internal routing is fine, you just need a suitable headset. Which is unfortunately pretty hard for this bike. But First C552 is one possible option. I'm still waiting on Token to launch their M-Box in IS52/40 though as it's a much better design in my opinion.
This is not good thinking. There is nothing about the internal headset routing that would cause the front end to be weaker. The fork is held in place with the exact same amount of material, the differences are in the c-clip for internal cable pass through and the top cap, neither of which is structural. The internal routing is offered as an option on the 909, 1001, and 1002 frames with no issues reported about front end failures.
edit: removed 1003 from list
