If your emails are in anything other than mbox format, then notmuch will not modify your email files - it merely builds an index for them so you can query. That should take care of your search needs.
As for HTML email, if you mean HTML converted to text, then notmuch will do it. If you mean show it as proper HTML, it won't. It can also show images inline (although my setup stopped years ago and I haven't debugged why). To be frank, I don't like how it converts an HTML email to text - it doesn't even preserve links (i.e. it shows the text only, and not the URL it links to). I need to look into how I can improve it.
But despite these headaches, I still use it. It's good.
As for HTML email, if you mean HTML converted to text, then notmuch will do it. If you mean show it as proper HTML, it won't. It can also show images inline (although my setup stopped years ago and I haven't debugged why). To be frank, I don't like how it converts an HTML email to text - it doesn't even preserve links (i.e. it shows the text only, and not the URL it links to). I need to look into how I can improve it.
But despite these headaches, I still use it. It's good.