Let's assume that the situation for periods, exlamation points, question marks and commas is pretty well decided (we can get back to them if need be) and that “;” is used in connection with ni' to indicate displays within or at the end of matrix sentences. We need only be concerned with displays that are text here and we focus on right hand end problems for the most part.
In a simple case, like “She told me John is coming” 'meli li toki e ni tawa mi: jan Jon li kama.'. there seems to be no problem since the display and the matrix end together. But we might want to keep 'ni' and colon together and so try 'meli li toki e ni: jan Jon li kama tawa mi.'. But this looks like “She said that John is coming to me”, possibly a quite different claim. Putting a comma in to prevent 'tawa mi' from connecting with the display doesn't help, since terminal prepositional phrases are are already (optionally) set off by commas. So we need a way to mark the end of the display here. Or, of course, simply not allow this construction. We might, of course, use a period after 'kama', but that tends to end both display and matrix and leave the PP floating with another period unaccounted for.
But even if we adopt this latter approach, problems remain. Consider “She said that John is coming and Mary is going away” 'meli li toki e ni: jan Jon li kama. jan Mali li tawa weka.' As it stands, this is indistinguishable form “She said that John is coming. Mary is going away.” since the first period can be taken (as above) to end both the display and the matrix. To prevent this, it has been suggested that priods within a display be replaced by semicolons (;), so the above becomes 'meli li toki e ni: jan John li kama; jan Mali li tawa weka.' with the only period ending both display and matrix. The semicolon might be used in the earlier example to end the display (in place of a period) but not the matrix, but then the semicolon gets used to mark the end of the display, exactly what we were trying to avoid in the complex report case.
There is the further problem of what to do if the displayed text is not declarative: “She wondered whether John would come” 'meli li pilin e ni: jan Jon li kama ala kama*' The asterisk here marks an uncertainty about what to put there by way of punctuation. The display calls for a question mark; the whole calls for a period. Which wins out or do we use them both (?.), which looks odd. Of course, here we can say that the question doesn't really need a question mark since its status as a question is on its face. But suppose it is a choice question “She wondered whether John would win or Sam would fall apart” 'meli li pilin e ni: jan Jon li sewi anu jan San li pakala'. This is indistinguishable without a question mark from “She thinks that either John will win or Sam will fall apart.” so we at least occasionally need a question mark (or something). Similar problems would arise with exclamation points, of course, though those don't seem to occur often in displays.
Even with declarative sentences there are two further problem, displays within displays and conditional sentences. Consider “She believes that he thinks John thinks Mary is coming but that he is wrong” 'meli li pilin e ni: mije li pilin e ni: jan Jon li pilin e ni: jan Mali li kama; taso ona li lon ala.' (or so, given the problems cited). As punctuated, this seems to say the guy thinks that that John is wrong in what he thinks about Mary. So, the semicolon closes the display from 'jan Jon li pilin e ni:' and the period closes both the display from 'mije li pilin e ni:' and 'meli li pilin e ni:' and finally the whole claim. But how would one say that the guy is wrong in is belief about what John thinks? The words could be the same, but the punctuation would have to be different, somehow closing off the display from 'mije li pilin e ni:' (and so, hopefully, also from ''jan Jon li pilin e ni:') but not from 'meli li pilin e ni:' (since closing that would mean that she was wrong about here complex belief). A period after 'weka' seems to close too much; a semicolon doesn't seem to close enough.
Finally (for now, at least) consider “If she thinks that he will come, she will dress up” and “She thinks that if he is going to come, she will dress up.” Punctuation aside, these are both 'meli li pilin e ni: mije li kama la meli li len pona'. They differ in where the display ends, after 'kama' or after 'pona'. Of course, the first could be written as 'meli li pilin e ni la meli li len pona: mije li kama' but tht is getting to be too remote from 'ni' to be readily intelligible – or created on the fly. Again, we can try using a semicolon here, after 'kama' to mark the end of a display, but we still need it – or something – to mark the end of a sentence which is not the end of a display. We can't use a period after 'kama' as that seems to end not merely the display but also the matrix and so we are left with a floating 'la' and a following sentence. Perhaps that very fact would allow us to use periods here (and also in the first example), but it seems likely that further cases could be found to invalidate this use.
On the whole, an explicit “end-of display” marker – and one that is repeatable to cover all the preceding colons – seems the most complete solution. Pilo has suggested “--” but other suggestions are welcome.