I think that they should be allowed.
I have seen a couple of people get nasty over someone recommending a service in their blog but not disclosing that the link was an affiliate link. They were basically accused of being greedy. Which is pretty funny to me because Steemit kinda encourages that with the whole 'get paid to blog' bit.

I could see it possibly becoming a problem if people were putting affiliate links in comments. Like where someone is blogging about how their arthritis is acting up again, and then another person posts a link to a product that they say will help but with an affiliate link. Now of course this could be genuinely helpful advice, but it could also be abused.