Hello,
well, probably Booking cannot work with sh404sef without a special extension.
Similar as are needed for other more complex components, and as we offer for JoomSEF.
Therefore, you will need to disable SEO URLs through sh404sef for Booking componnet or adjust its configuration so it works using just a component router.
I am not sure if sh404sef allows that, JoomSEF does for sure.
Another options is to have an extension for sh404sef created, that would ensure the compatibility.
JoomSEF allows both modes - it can work with the component router, plus there is a special extension for Booking for even nicer SEO URLs, that are further fully customizable.