Company I work for will plan me straight through a tropical depression because their books say they can. Unless the storm system is declared as a Cyclone, Typhoon or whatever then they'll plan it. Can get interesting, particularly if you're unlucky enough to be enroute and the weather folk sitting comfortably on the ground declare the system is now a Cyclone. Bit late then I'd say. I've seen ISA deviations from +15 (typical in the area I fly) shoot up to +30 when flying over tropical circular Lows and these weren't fully developed storm systems. A few hours later they were. Documentation I can't provide but watch out for the temperature rise if trying to climb above these weather systems. It's worth having a read of your company ground planning manuals about their reasoning on planning of the route. The devil could be in the detail.