Yeah, but with 3rd Party apps other things/factors are mixed into the equation. If both sites were WordPress then you would not be having this issue. In any case, it is ALWAYS better to compartmentalize .htaccess control to each website/folder (mostly for sanity sake/keeping track of what is doing what) by actually controlling each site with its own .htaccess file/code/rules. So since the image library 3rd party app already has an .htaccess file in its folder then what you want to do is add hotlink protection code in that image library .htaccess file.
Logically you will not have to do anything else with the WordPress site’s .htaccess file/code since what will happen is the /imagelibrary/.htaccess file will control what referers are allowed to link to images. In the event that the WordPress site’s code is still interfering with that image library htaccess file then you would use a 3rd party rewriterule in the WordPress htaccess file for the /imagelibrary/ folder as shown in the link below.
http://forum.ait-pro.com/forums/topic/custom-applications-outside-of-wordpress-3rd-party-apps/