When the Permalink Manager was first designed, it was supposed to be used for a typical WordPress website, which usually has less than a few thousand subpages. As a result, all custom permalinks are saved in a single row in the database in order to avoid slowing down the pageload with multiple SQL queries to the database. This is the most effective approach for small and medium-sized websites, without affecting site speed.
While this data structure works for the vast majority of WordPress sites, it may not be optimal if you want to use the plugin to rewrite tens of thousands of permalinks. What works well for a smaller website may not scale well for a megasite. When the number of addresses on your site exceeds tens of thousands, the custom permalinks array may become quite huge, and any operations on it can have an effect on pageload time.
To summarize, the plugin is suitable for small and medium-sized websites. It will not slow down your pageload time or affect its usability in any way. However, if you want to use it on a much bigger website with thousands of permalinks (more than 60.000), please consider excluding content types that do not require customized permalink format in order to lower the custom permalinks array. For further details on the plugin's performance, please visit this post.