Found issue in 0.5.6 and confirmed still exists in 0.5.9.

Multiplayer - Multiplayer option on hosted server, same fishing setup as single player (see below), reel in a Neptune Bounty chest and nothing in it. Something with multiplayer option is conflicting with the chests. Opened up over 20 chests. Tried on different days and after server restarts. Items are showing up in JEI with recipes. Confirmed with Server Admins that they have not made any changes to the pack.

Single Player - I tried out fishing with the aquaculture2 fishing rods, tackle box, hooks, etc., and the Neptune's Bounty chests have items in them. (one neptunium item and misc ocean items (driftwood, sea grass, etc.)). So the issue is isolated to the multiplayer option.

Thank you for the report, I will investigate the issue.