Not particularly, no. Junkyard engineering can be fun, though.
One of the reasons the rats nest deckplans seen in Traders and Gunboats are aethetically displeasing is that they give a junkyard engineer nowhere to go ergonomically. If new designs don't convey a proper sense of "everything in its place" then it becomes difficult for me as a referee to convey that the old wreck the PCs just boarded was obviously rearranged by a nutjob with a cutting torch and the gleam of inspiration in his one good eye.
Since deckplans are ubiquitous in MGT, you have the opportunity to put some color into your remodelling. Start with the original deckplan and a list of the component volumes that are changing due to refit. Start by penciling in moved bulkheads, new hatch locations, and removed staterooms etc. This is a first pass, but its worth keeping. Now do it again, but with an eye toward the first one and the things that don't look right. Effectively you are fixing the fixes.
With two or three iterations available, you now have several scenarios available to inflict on the PCs. If they want a refit quick and dirty (and cheap), pull out the 1st pass ergonomic nightmare. If they want to let a naval architect redesign their ship to look like the refit is the original fit, then they get to spend more time and money getting it done, but they won't be doing the steeplechase to get from one end of the ship to the other...