You cannot solve when making the PDF, because if fine in Acrobat, then the link is OK. You also cannot prevent it from opening in the browser, because the browser handles how to open PDFS. The browser included PDF readers can be switched off or there are (probably) settings to always open the PDF in an external application (Adobe Reader etc.).
However, I also create PDFs from within Indesign (though not interactive ones), which include hyperlinks for e-mail, and put them on our website. If I use Chrome and click on any PDF link, it opens in the browser and hovering over an e-mail address reveals the mailto: link (subject not included, doesn't matter anyway) and a click opens my e-mail client. Works perfectly.
Can you provide a link to one of your online PDFs for testing?
If you go to your browser (at the moment I'm using Firefox) and go to options and Applications. You will see what file types are opened by what program.
Browsers for some reason are building their own PDF readers, like FoxitReader, and Chrome has their own, and I think IE has one, problem is that 3rd party pdf readers don't include all the modules for a PDF, so certain aspects can appear incorrect or fail to function at all.
It's best to include a line with the link to the PDF that it's best viewed in Acrobat Reader and provide a link/badge to download reader. Or a link to instructions to change the default program for opening from the Browser options.
Thanks. We're a university and we send out a lot of e-invites and e-ads. Most people have no clue whether they're looking at a pdf in their browser or Acrobat Reader. Since there's no way to adjust users' browser settings, we will just have to live with the fact that the email subject won't fill in when clicked on from a browser view. Thank you for confirming what I suspected. No work-around.