Why is %used higher than 100 in esxtop?

As per https://communities.vmware.com/docs/DOC-9279

%USED is the percentage of physical CPU time accounted to the world. If a system service runs on behalf of this world, the time spent by that service (i.e. %SYS) should be charged to this world. If not, the time spent (i.e. %OVRLP) should not be charged against this world.

So ideally, %USED = %RUN + %SYS - %OVRLP

However, why does this value exceed 100%?

The answer simply is Turbo boost.
%USED is proportional to any processor frequency scaling and varies accordingly. Also, %USED decreases when hyper threading is enabled or if power management is enabled. In cases where the CPU frequency is scaled down, %USED will be less than 100%.

Therefore if you are looking at %USED when troubleshooting performance issues, accommodate any power management or turbo boost that may be enabled on the host.