Is there a stigma to writing/publishing erotica? If it is my interest to ultimately be successful in some other mainstream genre (YA for example) is it something I should avoid at all cost? I realize a pseudonym was probably once the answer to avoiding any potential taint, but in today's internet age, I have my doubts as to the the anonymity one would actually provide.
50 Shades of Gray isn't the comparison if you're thinking of publishing erotica. 50SG is a phenomena that we're not likely to see repeated for quite some time. And if you were the author of a book that successful, you'd have a whole different set of problems than trying to be published in another category.
Erotica is a large and thriving category, thanks in large part to electronic publishing. I think you can have a very nice lucrative career writing erotica without worrying about whether you can be published in other areas.
That said, you're right that you'll want different names. You really don't want your YA readers and your erotica readers going to the same website for info about the author. For starters, your YA readers will want to interact with you; you may not want your erotica readers doing that!
The trick is to separate the identities completely. You can register copyright to a business name; you can open a bank account in a business name, and have 1099s sent to a business name. Yes, someone could track you down and discover the name behind the corporate name, but that's a feverish stalking we're not talking about here. We're talking about a general knowledge that Felix Buttonweazer is the same person writing Pat The Bunny and Bunny Does Boston.
Make a plan about separating your identities and get all the pieces in place BEFORE you sign a contract and you'll be fine. (If you have an agent, s/he can help you with this.)