I know this is an old post but this limitation still exists in Notepad++. Besides Sri Varshan's suggestion, another option is to use a plugin named NPPTaskList, which can be downloaded here. It is designed to work like a to-do list but can work nicely as a bookmark list as well. Just install it like any other Notepad++ plugin and edit the npp_task_list.cfg file to use whatever "$" patterns you want; the default looks like this:
Any line that includes one of the above keywords (really the pattern sequence that begins with "$") will be included in the Task List, which is a sidebar. For example if you are coding in VB and enter this line:
REM $NOTE: This is a "bookmarked" line of code.
... it will show up in the Task List as:
$NOTE: This is a "bookmarked" line of code.
You can use these to navigate around your document by double-clicking them in the Task List.
I haven't tested this plugin extensively but so far it seems stable.