1. A non-volatile storage system capable of reducing interrupt overhead, comprising: an interface configured to receive a command from a host device, the command including an identification tag, the identification tag chosen from a limited set of identification tags, each identification tag being unique to an outstanding command, the interface additionally configured to schedule host data transfers using a host communication thread, the host communication thread configured to produce an interrupt upon host transfer completion; and a processor configured to manage communications with the host device through the interface, to determine whether to place the command in a first queue to be executed based on an available capacity of the first queue, to place the command in a second queue if it is determined that the first queue is filled to capacity, and to, upon placing the command in said first queue, selectively disable generation of an interrupt by the interface upon host transfer completion, said interrupt indicating a completion of a data transfer to the host device or from the host device, the selective disablement based at least in part on one of a command type, availability of interface resources to accept additional host transfers, and a command size, whereby the selective disablement reduces an overhead associated with executing the command.