It seems there should have been protocols to examine anything alien item brought on board a starship.
This just doesn't sound practicable.
There are a thousand people serving or living on that ship. All of them supposedly move back and forth at irregular intervals, on business, on leave, on missions. All of them supposedly have luggage. We've never heard of anybody being interested in examining that luggage: Guinan can bring aboard any liquid toxin she wants to, Admiral Quinn can bring along his favorite parasite, and nobody examines Beverly Crusher's tennis racket or her son's nanites for their weapons potential. And rightly so, for a number of reasons.
1) Odds are, 98% of everything brought aboard is "alien items" rather than Earth items. What difference would that make anyway? Why can't Earth technology be dangerous or evil? Why should alien technology be?
2) Starfleet's job isn't to examine consumer products to make sure they are safe for the consumers. Starfleet might be interested in stopping said products from being used in evil ways, but that won't be done by prohibiting the products - one doesn't confiscate kitchen knives from households, one patrols the streets for knife-wielding maniacs, or jails as a deterrent those who have already wrongfully wielded the knife.
3) Besides, the E-D is a warship. It would be a bit absurd to forbid people from bringing aboard penknives and the like when they can walk to the weapons locker, punch in their authorization code, and extract a handgun that can melt cities.
4) Even if one doesn't exploit the violence potential of a warship, one can exploit the manufacturing capabilities of a starship. There's no point in stopping somebody from bringing aboard, say, a spying sensor because one can build such a thing aboard just as easily, out of innocent components including ones that were already onboard. It may be practicable to stop somebody from arriving with a fully loaded phaser bazooka, but that can never stop a person from having a fully loaded phaser bazooka at his or her disposal later on. Anything is a potential weapon; something brought in by your trusted but adventurous First Officer is probably
more likely to be a potential weapon than not, but at the same time it poses little or no risk to anybody, due to how it was brought aboard.
Timo Saloniemi