In general casting from a magic item is imperceptible, but it depends on the magic item
Xanathar's Guide to Everything gives us the general requirements for spellcasting to be perceptible:
To be perceptible, the casting of a spell must involve a verbal, somatic, or material component.
The Dungeon Masters Guide gives rules for Magic Item spellcasting (emphasis mine):
Some magic items allow the user to cast a spell from the item, often by expending charges from it. The spell is cast at the lowest possible spell and caster level, doesn’t expend any of the user’s spell slots, and requires no components unless the item’s description says otherwise.
So, by default, casting from a magic item is imperceptible.
For some items a specific, perceptible action is, however, required to cast the spell from it:
Activating some magic items requires a user to do something in particular, such as holding the item and uttering a command word, reading the item if it is a scroll, or drinking it if it is a potion.
Uttering the command word, or reading aloud from a scroll would be perceptible enough, at my table, to enable counterspell to be used.
Similarly if a spell cast from the magic item requires one or more components (as listed in the item description) it would be perceptible for the purposes of counterspell, at my table.
The effects of the spell may tip an observer off that magic is afoot after the fact
If the spell is counterspellable it would be reasonable for someone to know that a spell has been cast.
Similarly if the spell produces a noticeable effect, like magic missile or fireball, then it is perceptible to an observer (but not necessarily counterspellable depending on the circumstances).