Bob,
The arguments and discussions presented on this subject are again numerous and debatable.
As you rightly point out the density of the acrylic is insufficient occasionally to hide the visible brass tube. Firstly consider the pen that you are trying to create - are you making a rod for your own back? Compare the Sierra, uses a 27/64 drill bit with a finished thickness of the pen of around 13.1mm The drill (10.65mm) dimension taken from the finished dimension and then halved, means that you have 1.22mm of material in the middle of the pen at best, I think the bushings from memory are 12.15mm so at the ends of the pen the thickness of the material is less than half a mill. Is it wise to put the most translucent acrylic on this pen? If you are after the same style of pen then try the Lucida from TB or the Berea equivalent, the Aero Pen. Think from memory that it uses a 21/64 drill bit (8.3mm) and has a similar finished dim of 13.1mm (far superior mechanism as well) The finished thickness in the middle of the pen is 2.4mm thick, some significant difference from the sierra 1.22mm!
First step was consider the pen and the translucence of the acrylic and now the gluing. The things that you are going to stick inside the acrylic are, the tube, paint, glue.
I paint the tube by priming it and then overspraying it. I use car primer and spray, there are more that work.
Glue. Some argue that if you paint the tube and not the blank then you can see the glue (I would suggest that you've got the wrong blank on the wrong pen if you can see that clearly but the most important thing is that you can only read the difference of where the glue is and where it isn't and to that end you havent got equal and total glue coverage on the inside of the blank which is a bigger problem)
Painting the inside of the blank which Brian and others have suggested you can achieve with a cotton bud or similar is a counter to the issue of visible glue.
I have double drilled my acrylic blanks firstly with a smaller drill than the final diameter and then the second drill at the right diameter. This I find gives a smoother inside to the blank whcih does several things, it makes equal glue application easier and as the inside of the blank is smoother, it doesnt scratch the paint off the tube if you have painted it. By way of experimenting, drill some off cuts and then insert the tubes partially to see how smooth the inside really is. Drill speeds are important to keep the acrylic from softening as the re hardened material also proves a hinderance to smooth glue application and paint retention.
I'm yet to be convinced that there is any better glue to use than Epoxy when gluing wood or acrylic blanks, I find that I get better coverage with epoxy, pu is a nightmare across the board.
Paint the inside if you like and feel better but I would look closely at the blank and pen style.
So, in answer to what was a brief question to which I have given a lengthy opinion, not answer, I hope this helps, if not just ignore it!