If you like The Shadow Thieves
The Shadow Thieves by Anne Ursu is part of a series (The Chronus Chronicles) so you may be interested in book 2, The Siren Song, if you haven’t already read it. Since you mentioned liking historical fiction and since The Shadow Thieves (and Percy Jackson) have mythology, I’ve included some books below that have both of these and also a couple with a little fantasy/magic. Here are some other books that I hope you will like:
Pirate Curse (Wave Walkers, book 1) by Kai Meyer.
In a place similar to the 1706 Caribbean, two fourteen-year-old "polliwogs"--humans who can walk on water--rely on a mysterious figure
known as the Ghost Trader and a band of pirates to help them escape from the evil that is chasing them.
The Night Tourist by Katherine Marsh.
After fourteen-year-old classics prodigy Jack Perdu has a near fatal accident he meets Euri, a young ghost who introduces him to New York's
Underworld, where those who died in New York reside until they are ready to move on, and Jack vows to find his dead mother there.
The Akhenaten Adventure (Children of the Lamp, book 1)by Philip Kerr.
When twelve-year-old twins Philippa and John discover that they are descended from a long line of djinn, their mother sends them away to
their Uncle Nimrod, who takes them to Cairo where he starts to teach them about their extraordinary powers.
The Witch's Boy by Michael Gruber.
A grotesque foundling turns against the witch who sacrificed almost everything to raise him when he becomes consumed by the desire for money
and revenge against those who have hurt him, but he eventually finds his true heart's desire.
The Red Necklace : a Story of the French Revolution by Sally Gardner
In the late eighteenth-century, Sido, the twelve-year-old daughter of a self-indulgent marquis, and Yann, a fourteen-year-old Gypsy orphan raised to perform in a magic show, face a common enemy at the start of the French Revolution.
Inkheart by Cornelia Funke.
Twelve-year-old Meggie learns that her father, who repairs and binds books for a living, can "read" fictional characters to life when one of
those characters abducts them and tries to force him into service.