I always get huge (unbelievably huge) W&T bills after long FSD flights (where target station is many light minutes away from beacon).
Just got to Haiden, the one Station they have there: 58k W&T repair! Short stints do almost nothing, a couple of thousand max. So my current hypothesis is that it's connected to presumed damage from hitting stuff at high speed (dust, debris particles, hard radiation) - which is exaggerated when you FSD-cruise at over 1000c, as I did for that run. I had no visible damage whatsoever, hull and all components at 100%...
It's still way too high, though!