As others have noted, there is an easy way to get custom URLs into an Evernote note (and they work!). If this is actually a security issue, then Evernote has a huge security problem. But I don't think it's an issue. Just copy and paste your custom URL into a TextEdit, and TextEdit will create a clickable link. Then copy and paste that link to Evernote.
This requires a slightly annoying extra step, but it's a quick extra step.