For low self-esteem there is nothing you can say - wives tend to believe, since you're they're husband, you have to say positive things, so you don't count lol... Best thing my wife did was get a gym membership. Even though it has not really had much impact on her physical appearance (which was already better than most other woman her age) just going and exercising has made her feel a lot better about herself.
For hormones, you could try DHEA, which is available without a prescription and is a hormone precursor. Depending on the exact source of the issue it may or may not help and she might need actual hormone replacement. For my wife, she had low DHEA, which was causing reduced hormone production and taking an over-the-counter supplement seems to have helped. At least, since she started taking it, we had sex twice in a week for the first time in forever.
To get your wife's hormone levels checked, she will need to ask to get that specifically tested, they don't usually check that in a regular blood panel.