SkipHooks option also skips the creation of Notes

[kacper]

I used skipHooks => true when saving entity in one of my Account's Hooks. Due to that Notes are not created for this entity.
If I remove skipHooks=> then starts infinite loop which creates thousands of new records.
Is it possible to use skipHooks and create Notes at the same time?
If not is it possible to detect if Hook is executed more than one time during request?