No, they can't. Ki Focuses can only take Ki Focus enchantments.
However, assassins can use weapons with their own bonuses (and can use them as implements).
So if you think that your Assassin is better off with a magic weapon (and it's enchantment) than a magic ki focus, you should use the magic weapon. The advantages of the ki focus are that it:
Allows you to switch easily between weapons -- so you can pull a dagger and throw it, (or shoot some arrows) then pull a greatsword once you switch to close to buff up your basic attack, all using the magic bonus/properties of your ki focus. Or when things get roleplay-y, show up unarmed to the battle, and grab the weapon of the first thing you kill. Monks/assassins make great Improvised Weapons fighters, as their improvised weapons get their enhancement bonus.
Lets you apply its bonus to multiple weapons at once -- really useful for twin-striking multiclass assassins (or melee rangers who multiclass into Assassin to save on equipment costs).
Also, there are some sweet Ki Focus enchantments -- Final Sleep is Vicious, one level higher and with a cool property added in. Hawk's Talon has a good critical die and other nice properties/powers for a striker. Iron Body has an excellent critical die and an amazing property.
But there's nothing stopping you from building an Assassin who uses a specific magic weapon as her main weapon and implement -- maybe with a backup Ki Focus so she can use its property if the one on her main weapon isn't the best, and can pull thrown weapons if she needs a ranged weapon to trigger her shrouds.
