Does a negative interest decrease the money supply?
Definition of Money Supply:
The money supply is the entire stock of currency and other liquid instruments circulating in a country's economy as of a particular time. Because of it's definition, the money supply can only be affected if a central bank prints or burns currency. Thus, technically, rates don't affect it per-se. 

Velocity of money and money in circulation:
What you may be thinking of is related more with how much money is in circulation and how fast it changes hands. 

Effect of negative rates:
In theory, when rates go up, money flows into bonds and "leaves" circulation. By the same logic when rates go down, money flows out of bonds and "enters" circulation.