Saddle up!

It should not be a problem. The only problem it might cause is a buzz where the saddle meets the bridge, but you would hear it. So as long as it sounds okay you're good.

 

With the saddle bottomed out, the break angle of the string over the saddle is likely to be less than optimum. That can result in some string rattle and some loss of transfer of string vibration to the body. Whether the latter is important or not is a matter of debate, however most luthiers recommend a break angle of 15 degrees at a minimum.

Why the reticence about installing a shim?

 

You can totally just stick a bit of business card in the neck pocket and be good to go. Won't do any harm at all as many of the people on this board who have done it many times will attest.

If you bottom out your saddles the break angle probably won't be optimum, but it doesn't matter so long as it sounds good. You would hear any of the problems it could cause. On a guitar if you put it too low it can start to sound kind of like a sitar all warbly and buzzy but I've never seen that happen on a bass. Could happen though, I guess.

 

Let's address these things as you raised them.

If nothing else changed, removing a neck and re-installing it will not cause fret buzz to suddenly occur. But it can cause you to be leery of removing a neck again. I suspect that the neck screws were threading into the body as well as the neck. That will prevent the neck from seating properly and that could be the source of the problem. It's very common. When you take the neck off check that the screw slide through the holes in the body - if they don't, drill them out to a slightly larger size so the screw can be pressed through rather than threaded through.

I wouldn't worry about the wood on the underside of the neck where it joins the pocket. There's a finish in it that will inhibit moisture gain or loss.

Shims do not cause relief in the neck. That is entirely controlled by the string tension, the stiffness of the neck and the action of the truss rod. The shim has no effect on relief.

There may well be enough break angle with the saddle bottomed out on your bass. It will be less than I would like, but unless you are experiencing buzzes or rattles I would not be concerned.

 

Nothing to do with relief.

I used an old credit card though, those made out of stiff plastic, as a flat shim in my neck pocket as I had a similar problem, and it works flawlessly and almost fitted the pocket perfectly.

 

A business card will do. Fender used anything at hand - sandpaper, cardstock, whatever. If it impacted their tone they would have used something else - they were after all interested in sales. If a credit card shim gave them a competitive edge, they would have used that.

 

Just remember to loosen the strings before attempting to take the neck off.

 

You mean you used a full pocket shim? Why? One piece of card would have been plenty if it was about 1/2" wide laid across the butt end of the pocket.

 

Straightening a bowed neck could save you from installing a shim.

 

I don’t think you understand the geometry involved. A partial neck shim will not affect playability any differently than a full neck shim. But if it’s working for you, stay with it.