>> I have read that there is a maximum amount of hyperlinks per slide show in powerpoint - is this true? and what is the maximum?
It's true, but the limit is the amount of data storage the links use, not the actual number of links, and it may also depend on how other features in PPT are using data.
>> I have done a very large presentation - if i break this up to individual shows will this mean each show has its own maximum and I can use a hyperlink in each to match to each show?
Yes indeed. You've got it exactly right. For example, you could have a main "menu" presentation with links to each "section" (where each section is in fact a different PPT file).
Put an End Show action link at the end of each of those (or just press ESC) and the "section" presentation will close leaving your menu presentation up and ready to launch the next section.
The hyperlink limit is a per *presentation* limit, so by splitting the presentation, you increase the number of links you can safely include.