I once spent an afternoon tracking down a "bug" as to why sales tax wasn't being calculated on LedgerSMB only to find out I had set the tax rate to 0 in the tax interface.... Ok, it was working as intended. I felt pretty sheepish too.
Also taxes with a rate of 0 are ignored specifically because sometimes sales tax structures change (as with HST consolidation in Canada) and consequently old taxes need to be retired.....