How did Thanos know the Tesseract would be with Loki on the Asgardian ship?

Thanos has been playing an extremely long game over the years with the Infinity Stones. He was the engineer behind most of what happens in the Infinity Saga as pointed out by Thor:

Thor: I have no choice. The Mind Stone is the fourth of the Infinity Stones to show up in the last few years. That's not a coincidence. Someone has been playing an intricate game and has made pawns of us. But once all these pieces are in position...

_{Avengers: Age of Ultron}

Thanos sent Loki to Earth with the Mind Stone and the Chitauri army to conquer it and retrieve the Space Stone. Considering how close of an eye he has been keeping on the Infinity Stones he probably knew that Thor and Loki returned to Asgard with the Space Stone. Even if not using the Space Stone to travel to Asgard and restore the Bifrost probably alerted him to that as well.

Now he's also spent some time with Loki and knows him for the trickster he is. He almost certainly knew Loki wouldn't have just left the Tesseract on Asgard to be destroyed. So his best bet for tracking it down is to check Asgard, he sees it is destroyed and so checks for any survivors and tracks them down. Once he boards the ship and finds Loki alive on board he almost certainly knows his best bet for getting the Space Stone is Loki. So it isn't necessarily that he knew Loki had the Tesseract, it's that he knew Loki was the most likely to have it.

The use of the stones can clearly be tracked, even after the fact. In Endgame, Rocket is able to compare residual energy signatures from the Snap to the use of the stones on a very distant planet:

When Thanos snapped his fingers, Earth became ground zero for a power surge of ridiculously cosmic proportions. No one's ever seen anything like it... Until two days ago. On this planet.

Consider that in the events of Avengers, the Tesseract was used to open the portal, it was then used to transport Thor and Loki to Asgard, and then later on Loki then stole it and presumably used it to get back to the ship after awakening Surtur in Thor:Ragnarok; that means the last trace of the Tesseract's energy signature is OFF Asgard. Even if Thanos couldn't track the energy signature of its presence on the ship, all he'd really have to logically do is put himself in a direct route between Asgard and Earth - the only 2 places the Tesseract has been used in recent history. I'd argue the fact that he just shows up at the ship and opens fire is meant to clearly indicate he can keep tabs on it at all times.

Prior to the events of Avengers, SHIELD had been making constant use of the Tesseract for Phase 2, allowing plenty of time for anyone to detect and get used to the Tesseract's particular energy signature. Vision was the Mind Stone, meaning that by simply existing, he was making use of it - and arguably, since Wanda's power came from the Mind Stone, it's possible her use of magic was also giving off similar energy signatures. The Time Stone was used in recent history specifically at the Sanctums.

In between the fact that Thanos has been orchestrating his moves so that he can get his hands on as many stones as possible (to the point of knowing that the Reality stone was with the Collector), and that all of the stones had been active in a relatively short time span (the early 2000s), he certainly would have had the technology available. Moreover than that, he previously had the Mind Stone in his possession, and we don't necessary know what he did with it prior to giving the Scepter to Loki. He does specifically tells Tony Stark in Infinity War:

You're not the only one cursed with knowledge

Let's also not forget that Thanos used Eitri and the dwarves to create the Infinity Gauntlet.

I thought if I did what he asked, they'd be safe. I made what he wanted. A device capable of harnessing the power of the Stones.

Something like that is pretty impossible without some pretty specific knowledge on what the power/energy of the Stones is.