How is money destroyed when banks issue debt?
Generally, people do not pay for bonds with currency (e.g. pound notes). They pay with bank deposits. This means that Y has lost a deposit.

If the deposit was with X, the deposit is just destroyed; X does not hold deposits against itself.
If the deposit was with another bank Z, bank Z loses the deposit, and it has to transfer the 100 pounds to X via the payments system. X will not hold a deposit at Z.

In either case, bank deposits are destroyed, and they are a component of the money supply.