Yes, that is a bit annoying as well, but I made my peace with that (Probably also because I'm not affected by it directly). But the "ton" is a constant companion, and when it then gets to "kilo-tons" it just breaks the entire SI-prefix system to bits.
In practice, I just think of it as two base units: grams for small masses (i.e. prefixes smaller than 1 aren't used with tonnes), and tonnes for large ones. (Though terms like kiloton and megaton may well be referring to the US ton (2000 lb) or the Imperial ton (2240 lb) rather than the Metric (1000 kg) one).
