The issue with nipples is that they use tapered fittings, i.e. the threads are tapered so the more you turn them the tighter they get. This makes them pretty good at not leaking. On the other hand, it means that you can't tell how many times you have to turn it before it does stop leaking - and if you are designing a piping system, you can't tell how strong the apes who put it together are going to be, so the overall lengths of your pipes are going to be quite variable.
So pipe sizes are nominal. A half inch pipe is in fact about 3/4" diameter. A nipple is normally described by the overall length, of which (in the case of a half inch pipe) about 3/4" or so is threaded on each end. Something like 3/8" of that thread will engage into a typical fitting, so the length between fittings once it is assembled will be around 1 1/4", plus or minus at least 1/4". Basically, you figure this stuff out on the fly while you are assembling it.
If you need things to be more precise than this, you need to use more accurate fittings. Swagelock (or similar) fittings are the next level up, and VCR's are better yet. VCR's are very accurate, while Swagelocks have a little leeway in their tubing length. Often people will put extensible bent sections in their tubing runs so that the whole thing looks tidy once they are done.
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