Is taking money from a store without the owner's knowledge, with the intention of paying it back later from one's salary, considered theft?

Taking money from someone who entrusted you with it is not considered theft that necessitates cutting off the hand; rather, it is a prohibited betrayal, based on the Almighty's saying: ﴿O YOU WHO HAVE BELIEVED, DO NOT BETRAY ALLAH AND THE MESSENGER OR BETRAY YOUR TRUSTS WHILE YOU KNOW [THE CONSEQUENCE].﴾, and the Prophet's (peace be upon him) saying: "Fulfill the trust to the one who entrusted you, and do not betray the one who betrayed you."

You must desist from this or seek permission from the employer. If he agrees, there is no sin. Otherwise, it is not permissible, based on the Almighty's saying: ﴿O YOU WHO HAVE BELIEVED, DO NOT CONSUME ONE ANOTHER’S WEALTH UNJUSTLY BUT ONLY [IN LAWFUL] TRADE BY MUTUAL CONSENT.﴾, and the Prophet's (peace be upon him) saying: "The wealth of a Muslim person is not lawful except with his willing consent." And your intention to repay the debt does not justify proceeding with it, as it is an aggression, injustice, and betrayal.