Word of God: Why yes, the writer too lazy to come up with names has watched the Deadliest Catch.
Double hit: One ship associated with Capt. Foster's group is named Time Bandit.
Captain Foster routinely trades cargoes with a fleet of ships with names derived from Deadliest Catch.
Johnny Cash: "A Boy Named Sue" gets a slight reference when Suzan "Stew" Pebble introduces herself to Forestwalker's extended family during a visit to the Folly.
Little Fuzzy seems to receive a passing shout with starstones. These precious gemstones glow from some internal mechanism. The original sunstones in Little Fuzzy would glow when heated by something as limited as the warmth of the holder's hand.
To which hir boss replies: "Don't tell me, he sidestepped to avoid a pot of petunias?"
Chapter 3 makes a lampshaded reference to James Bond.
Real Life photo-reconnaissance / spy planes, the SR-71 and the U-2. These two aircraft series are mentioned as being the names of 2 different strings of electronic malware that are causing starship mounted sensors to not detect objects that they should be able to find.
The Bunny Brothers pull off a hat trick with no less than 4 shouts. Admiral Kline does a double take and lampshades the fact that someone had a sense of humor.