You means you
As comments to the original post point out, maintaining invisibility while casting detect thoughts is difficult to do, but let's accept the premise that the target of the spell cannot see (or presumably hear) the caster, even though the spell requires the caster to both see the target and be within 30 feet upon spell casting and to maintain that proximity, if not visual contact, for the duration.
In this situation, what does 'the target knows that you are probing into its mind' mean?
You are more than just someone
Spell descriptions in 5e are written from the perspective of the caster, and one would be hard-pressed to find a description without the word 'you' in it somewhere. So it could be that 'knows that you are probing' just means 'knows that someone is probing'.
However, consider the description of sending:
The creature hears the message in its mind, recognizes you as the sender if it knows you, and can answer in a like manner immediately.
Here, rather than simply saying that the target recognizes you as the sender, the clause is added 'if it knows you'. This directly implies that if you target a creature that does not know you, it will know it is being contacted by someone, but will not know it is being contacted by you. It's a bit of a stretch, but this could further imply that by leaving out the 'if it knows you' clause, detect thoughts is not, in fact, implying the target knows only that 'someone' is probing their thoughts. Instead, in detect thoughts the target really does know that you are doing so.
Tangential support for this interpretation also comes in the description of the dream spell. Here, the caster chooses a messenger - be it themselves or another willing creature. The messenger then contacts the target of the spell. Nowhere in the spell description does it say that the target of the spell recognizes the identity of the messenger, whether known or not.
If intentional, what does this mean?
5e does not necessarily have a level of editing and rules consistency that allows us to trust that the differences between these descriptions are intentional. We can agree that 'spells do what they say they do' - but did the writers really tell us exactly what they do? If we suppose they did - or if you, as a DM, want to play that they did - then in the case of a target contacted by dream, they have no idea who is contacting them. With sending, they know that someone is contacting them, but only recognize their identity if it was already known. And for detect thoughts, they know the caster, regardless of whether they are familiar with them or not.
So what does it mean to know someone you do not recognize? For me as a DM, I imagine it is a bit like receiving a phone call from someone you do not recognize. Their number is saved on your phone, so you 'know' who it was, and were they to call again, you would recognize them as the same individual, even if you know nothing else about them. Similarly, the person subject to detect thoughts who cannot see or hear the caster, can still recognize them as an individual, even if they know nothing about them. If they later see or hear them outside the spell, they will instantly recognize them - "So you're the voice that was in my head!" Recognizing in real life the magical character that was heretofore only in your dreams is a common enough trope, and as a DM I would lean into that sort of experience.