Here are a few things that my BBEG will use to "scry" on the characters.
Level 3 through 6
The boss will send scouts to find the characters. Among the scouts, a novice spell caster able to cast or use scrolls with the following spells: Long Strider, Invisibility, Sending and Sky Write. This is just a basic thing. The caster will use sky write or sending to warn the boss and the boss will use some scrying method on his minion, either Clairvoyance or Scry if high level enough or if the range is possible. This way, the boss will learn of whom are the caracter or at least see them. (A scroll might be enough to provide the means necessary to warn the boss).
Two cases at these levels are possibles (obviously more, but they are usually a combination that will include both cases)
The BBEG is aware of the group coming to his lair. Either through spies or some other means.
Then the scout party or individual will be only there to get a pin point on the location of the characters. No communication beside Sky write might be needed. The message might not even be clear. "The sun is glorious" seems inconspicuous enough that the players will not over react to such a message in the sky. Or "Nanny needs a cleric, send one at the village" might even derail the party from the boss' lair to investigate, allowing for a nice ambush.
The scouts might be there not only to locate the players but also to attack and kill them. If this is the case, the boss' main scout will not participate. He will observe and let the BBEG scry or clairvoyance the whole fight. The scout will then flee as fast as possible (staying invisible through the whole fight) Using Longstrider to start fleeing and then recasting invisibility (if needed) to get away. With a nice Detect Thoughts, the boss' will get a clear picture of the way the scout saw and analyzed the players. At this point, the players might become "know" for the boss or the DM might require more than one such encounter. In any cases, the boss knows the looks of the players.
The BBEG is not aware of the group coming to his lair.
Here the boss will not try to "ambush" the characters with spies and such. Usually, the boss might set patrols and such and such and one missing patrol might (or more precisely, will) start an investigation. This assumes that the players did encounter a patrol and slew everyone or mostly everyone.
Here the boss will use spells such as: "Augury and Divinations" if he has access to them to make sure that no one is coming to his lair. Naturally, a party of adventurer coming to kill you and your minions for an Augury spell will count as Woe for your BBEG. And thus, the BBEG will start to prepare for the arrival of the players. Patrols will be reinforced. And the lair itself might see some more guard duties.
If the players assault the lair and retreat. The boss will raise (if possible) fallen troops into undead. He will send S&D parties and if the players can't be found and made quite a dent in the lair, the boss will flee.
The main point of all this is the following.
If the player could and can do the same thing, you add a layer of belief to your game. It is easier to accept something you could do your self than a SUIM (Shut Up It's Magic) effect.
Also, it makes the DM appear fair and square. Not every vilains (BBEG) might have access to these methods. But mundane methods and magical ones can and will mix allowing player to "see" that nothing was expressively built around their party but made to "foil" any party. If it happens that one of your players has something that can foil some basic things and shenanigans, so be it, more power to them and an other level of belief is added to your game.