Search and pagination aren't yet supported, as Octoshop was originally designed for sites with a small number of products. If you're familiar with Laravel and Eloquent, you can use their docs to write your own code that searches and/or paginates the category/product tables.
For search, all you need is a component that takes the search term as input, then do something like
Product::where('name', $searchTerm) to find results that match. Check the tables in a tool like Sequel Pro (OSX only) or phpMyAdmin to see the exact field names. Pagination is easy too - there's a section of the docs dedicated to it.
Either way, you'll still be able to make use of the models provided by Octoshop to actually provide the data. All you need to do is write some code to "wrap" those models and tell them what you want.