The bridge is owned by the State of Maryland. Despite the name, Interstate Highways and the bridges that carry them are owned by the states.
As to why the bridge did not have any protection, after the Sunshine Skyway collapse, that would be a question for the Maryland Department of Transportation.
The main federal involvement would be the US Army Corps of Engineers which would be responsible for keeping the channel open and at the correct depth.
That is my understanding of things. Permits from the Corps of Engineers are required for almost anything touching a federal waterway. The Corps would have at minimum reviewed the plans and monitored the bridge construction from the perspective of protecting the waterway.
Were I investigating this, I’d look at the design/plans/constracts; the permitting/review process; and the communications between the various parties, to see if things were cut out of the project to save money. Or maybe things were in the contract scope but not actually done. Payoffs? If the State funded and built the bridge, but the Corps was in charge of the waterway, did pylon protection IN THE CHANNEL get lost in the responsibility shuffle?