Are you calling that code in a chunk that is cached?
Otherwise i've experienced this aswell and it seems custom placeholders sometimes behave that way, it's probably due to the fact that they actually have some unprocessed value during the IF computation but when it's actually output you see nothing. Or that the value is somehow "null" instead of "" while modx output filter might do a strict comparison.
If you're not calling it in a cached chunk or part of code, i suggest first trying with another getPage placeholder such as pageCount
or total
.
Like:
[[!+pageCount:gt=`1`:then=`<ul class="overview__pagination">[[!+page.nav]]</ul>`]]
If that still doesn't work, a last resort in the form of a simple snippet will always solve it, like:
[[!outputPagination? &total=`[[+total]]` &limit=`XX` &output=`<ul class="overview__pagination">[[!+page.nav]]</ul>`]]
In snippet:
if ($total > $limit) {
return $output;
}