<<Disclaimer>> I've never kept hamsters but I've had guinea-pigs for years.
I found the females pee loads far more than males. And when they're in season, their wee smells stronger. I clean the bedding (where they sleep/wee/pooh) every day (I have 5 piggies but even when I had 2 females I still had to do this)
She might be trying to overpower the lemon smell . I've never liked strong scented bedding or cleaning products for rodents. Their respiratory systems are very sensitive and their noses are right in their bedding. And IMO, if your pet smells so bad that you need to 'mask' it, you're not cleaning often enough. Is she drinking enough? Is her wee too concentrated? Are their other pets that she's maybe in competition with? Has her home been moved? Maybe she doesn't like her new site? Is she too near the TV or window?
I'm sure their are products like Megazorb (it's an equine bedding made from dust extracted wood fibre) that are available in more small rodents friendly quantities. Maybe something like that? (Megazorb is very absorbant and helps control the aroma)