If the non-shelter rabbit is a female, be aware that females *need* to be spayed for health reasons (unspayed females live, on average, half as long as spayed females due to their proclivity for cancers of the reproductive system) even if they're your only rabbit [males are primarily neutered for behavioral reasons, so if you only get one rabbit and it's male, neutering can be avoided if you can tolerate his hormonal behavior]... and spays are more expensive than neuters. I payed $30 each to get Nala and Gaz from a breeder (couldn't find a shelter in my area that had rabbits other than a rabbit rescue that refused to adopt them out because "too many got returned") - when they were 5 months old, I coughed up $465 for two spays... by comparison the male I got a couple weeks ago, Norman, set me back a "whopping" $30 adoption fee and came already neutered (I've moved since getting my girls, hence the sudden availability of shelter bunnies).
Between the stress, worry and expense of spaying/neutering and how obnoxious teenagers of *any* species inherently are, there's a lot to be said for adopting an already fixed adult rabbit from a shelter!
That said, I think you should pressure the shelter for more information before making a decision. Most rabbits prefer the company of another but there are exceptions and unlike some animals (rats, GPs, sugar gliders, etc.), most rabbits *can* do just fine on their own if they get plenty of attention and interaction. Also, the idea that M/F bonds are vastly superior to same sex bonds is a bit of a myth, albeit a wide-spread and partially truthful one - personality is what really matters. To be fair, the odds of randomly picking two rabbits with compatible personalities does seem inherently higher if they're opposite genders... but if the two personalities are compatible, that trumps their genders - my girls are proof of that, and many others here have a happy, same-sex bonded pair.
What I'm getting at is that, while I don't see any actual red flags, I do see some signs that make me question the shelter's knowledge in pairing/bonding rabbits - they could be following conventional wisdom (rabbits in pairs, only M/F bonds, etc.) because of personal opinion regarding what makes bunnies the happiest and because they've been bonding rabbits for a long time and are sticking with what's easiest/most reliable as a means of expediting the bonding process since they bond so many pairs... or they could be oblivious to the fact that every rule has exceptions because they're not actually as rabbit-savvy as they might think. It could very easily go either way and the only way to know is to ask a lot of questions.
Ask if the two rabbits are bonded. If they say yes, ask how long they've been living in the same cage together, if there have ever been any problems, fights, etc. Tell them you're new to rabbits and ask "Out of curiosity, what methods do you use to bond two rabbits?" (if you're unsure that their answer is a good one, feel free to ask us!). You could also mention that you're worried that going to a new home might upset their bond and ask if they would be willing to guide you through repairing the bond if the rabbits were to start fighting within the first week or two. If they can't offer a detailed explanation of HOW they bond two rabbits and/or indicate that you're on your own once you adopt them, that's a huge red flag and indicates that there's a good chance the rabbits aren't truly bonded even if the shelter swears otherwise. (Keep in mind, just because the shelter employee/volunteer you speak with may be clueless, that doesn't mean there isn't someone else there who knows what they're doing - if they can't answer and explain that someone else handles that aspect of things, ask them for the contact info for whoever bonds the rabbits and then track that person down for questioning.)
As for getting one vs two your first time, I jumped in head-first with two and I actually think it's a little easier that way (IF they're either fully bonded or are babies (since babies automatically get along) - having to bond rabbits right off the bat would be far more challenging than just dealing with one!). It's no harder to care for two than it is for one if they're living together. Having two rabbits gives you a basis for comparison - you're less likely to get worried about weird behavior, since if they're both doing something, it's probably normal. Also, most bonds have a dominant rabbit and a submissive one - a submissive rabbit on their own is often extremely timid, skittish and difficult to win over... but when they've got their dominant friend to show them the way, it helps them be more comfortable and outgoing. A dominant rabbit may be less likely to desperately want to be the boss of YOU if they have a companion, because they get to be the boss of the submissive rabbit - being in charge when she's with Gazzles definitely helps Nala accept that she can't be in charge with the humans!