George,
I believe you are correct in saying that there is no way to link directly to a specific anchor tag within an html file from the context help.
I would encourage you to visit our
Product Suggestion Center if this is a feature you would like to recommend that our R&D team consider for future versions of LabVIEW.
Is it possible for you to create a .chm file? Or perhaps you could have some kind of "table of contents" at the top of your .html help file. This would require an extra click by the user but may be an option for you.
Regards,
Simon H
Applications Engineer
National Instruments
http://www.ni.com/support/