I don't add mine automatically but I use my regular emails and etc. that I need to book the reservation. If the hotel finds my account and adds me in, so be it. I've never had a problem having the shops accepted with Loyalty Points.
The only time I think it becomes an issue is if you're a high ranked member of any Loyalty program, i.e. qualify for free breakfasts, etc. which could interfere in your ability to pay cash at the bar or when dining. (Un)Luckily, I'm not high enough ranked in any hotel loyalty program!