Just to clarify what's happening here:
A maximal lottery result can be something like:
A: 50%
B: 30%
C : 20%
where these are the probabilities of the candidates A, B and C being elected. So is non-uniqueness simply that sometimes there might be another probability distribution that is also optimal? E.g.
A: 55%
B: 35%
C : 10%
(Or maybe some sort of continuum of optimal results.)
You said that where preferences are strict and the number of voters is odd, there will be a unique solution. Is this simply because an even number of voters can lead to a head-to-head tie between two candidates, or is there something else more complex going on with an even number of voters? It seems intuitive to me that it's just because ties can happen.
In the case of ties, this isn't a problem unique to Maximal Lotteries. You can get ties in any voting method, e.g. FPTP and have to deal with that somehow. With a big election, ties will be rare. Obviously it's less likely with FPTP because it requires a tie at the top, whereas with Maximal Lotteries, there can be a tie between any pair of candidates potentially affecting the result.
It can be argued that in the case of more than one optimal lottery, it doesn't matter which one you choose because they are all optimal for the voters. Some will work out better for some candidates (a higher probability of election), but elections are about what voters want. They're not really about the candidates.
In the same way that a lottery generates the winning candidate, you can simply have a random mechanism to determine which lottery to use. I don't see this as a major problem in the general scheme of things.