The specific format of the filing against a specific item of property rather than suing the owner directly is called in rem jurisdiction; it's a legal practice that originally arose from the need to take action against property where the correct owner could not be identified (like a ship, or undeclared cargo).

There are several different reasons why the government might use in rem jurisdiction, but usually it's because it is the item itself which is in violation of the law rather than that a specific owner violated the law by owning or manufacturing it. So the case becomes one of civil forfeiture rather than criminal prosecution. The text of the 1906 Pure Food and Drug Act did allow for criminal penalties:

Be it enacted by the Senate and the House of Representatives of the United States of America in Congress assembled, That it shall be unlawful for any person to manufacture within any Territory or the District of Columbia any article of food or drug which is adulterated or misbranded, within the meaning of this Act; and any person who shall violate any of the provisions of this section shall be guilty of a misdemeanor, and for each offense shall, upon conviction thereof, be fined not to exceed five hundred dollars or shall be sentenced to one year's imprisonment, or both such fine and imprisonment, in the discretion of the court, and for each subsequent offense and conviction thereof shall be fined not less than one thousand dollars or sentenced to one year's imprisonment, or both such fine and imprisonment, in the discretion of the court.

In this case, United States v. Forty Barrels & Twenty Kegs of Coca-Cola, 241 U.S. 265, the Coca Cola Co. stepped up and became the claimant of the property, but it didn't have to; if they did not, they would have basically forfeited the property without a legal fight, and perhaps worse than that would have opened themselves up to more seizures under the Pure Food and Drug Act, as the legal question of whether the Coca Cola violated the law would not have been challenged in court. If they did step in, then the Coca Cola Co. opened themselves to being liable for the costs of the case if they failed.

In discussing the legalities of the act, it's notable that many cases were made in rem, specifically with an eye toward the seizure (and eventual condemnation) of the foodstuffs. You can read the opinions in Decisions of Courts in Cases Under the Federal Food and Drugs Act where the judges involved specifically note this as a reason for using in rem jurisdiction rather than applying criminal charges.