Is it realistic and advisable to ask when channeling the deep subconscious to protect itself from outside intrusions? If so, what is the most effective way to do so?

The best and most effective way to encourage self-protection is to instruct the deep subconscious to always ask the higher self for a yes or no designation about any approach by outside consciousness, to tell the deep subconscious whether this is a safe consciousness to partner with and engage or to resist because it is an undesirable being to cooperate with. This will go a long way to keeping up a perimeter of safety, so to speak, so the deep subconscious is not completely vulnerable, being isolated as it is, through the disconnected state from higher oversight and guidance by the conscious level of the mind.