I highly doubt that "half" of all Hudson and New Haven trains would terminate at Penn Station...
Well, if the trains were split by suspected destination of the riders, the number would be 30-40% to Penn Station.
According to the CT presentation from March 2013 on the MTA website, the proposed plan is to run 6-10 peak hour New Haven Line trains to NYP, 4 trains/hour reverse peak direction, and 2 trains/hour off-peak and weekends. But the EIS may have revised those numbers.
Of the proposed 4 stations in the Bronx as of the 2012 presentations, the Hunts Point MNRR station would be adjacent to the 6 Line Hunts Pt station, although with a pedestrian path under the elevated highway. Quoting the slide bullet, the station features include: "Transfer location between the NYCT 6 Line and the New Haven Line creates a new transit hub." Which strikes me as creating a possibility for the station to become an Amtrak stop for faster Boston trips for those living along the 6 Line rather than going to NYP and then making the slow trip through the East River tunnels and Queens.