Regarding the size of ships, it seems like nowadays more often than not the only significant larger vessels to come up the Potomac are tall ships coming to Alexandria. I don't know how tall their masts usually are, but it's hard to imagine the Nice Bridge's proposed clearance of 106.5 feet would be that big of a deal. Note, also, the Washington Navy Yard is unlikely to be an issue because the new Douglass Bridge over the Anacostia River is to be a fixed span (the current one is a swing bridge); this is one reason why they had to move the USS Barry out of there when they did, so that it wouldn't get stuck upstream of the new Douglass Bridge. Having the fixed Douglass Bridge effectively means there won't be anything taller than its clearance going to or from the Navy Yard, and it's pretty certain that bridge will have a lower clearance than the new Nice Bridge will. I kind of view it from the assumption that the approval of the Douglass Bridge design is effectively an acknowledgement that the Navy Yard is no longer a navigational issue.
froggie would know better than I, but I believe there is no shipping activity from the naval facility at Indian Head. I can't enter that facility, but a look at a satellite view reveals no infrastructure for vessels. It looks as though the Dahlgren facility probably doesn't have that sort of activity either. The significant port around here is really Baltimore.