I have more or less the same problem with my girlfriend. I'm the one who doesn't speak up often, and she's the one asserting her needs or opinion strongly. I'm going to offer you more of a framework in which to work with your wife than an actual "do this" answer.
I am a straightforward guy and I speak up as soon as there is something that I think is wrong and say why. But I realise that sometimes that hurts her. She told me that, in the past, I was sometimes verbally aggressive when we disagreed about something, and now she fears that and she's not willing to challenge me.
I think that there are some point here you can work on:
How do you express your thoughts? I noticed that I tend to think that my girlfriend's opinions have more value because they are more strongly expressed than mine. I'd use her same level of strength for more important matters, so it happens that I measure her expressions with my strength scale and instinctively think that she must attach a lot of importance to her opinions and that it's better if I not challenge them. When I confronted her on this topic, she was completely taken aback and explained to me the real strength of her statements.
What you can do is add nuance to how you express your opinion in order to soften them. Instead of just saying "[x] sucks", add maybe's, specify that this is just your opinion and why is that, say that even if you don't like it it's not a big deal to live with it. I catch my girlfriend doing it and it gives me some courage to speak up and a measure of her efforts in including me in the decision making process.
What exactly does she fear? I think you should investigate this matter a little bit. Every reaction is different: not every people faced with perceived aggressiveness are afraid to speak up as a result.
What in her story makes her so afraid? What does she think the consequences will be? Try and see whether they are irrational fears. For instance, in my household dissent was treated with silence, so I subconciously tied expressed dissent with something severe happening to the couple, whereas my girlfriend's parent would never tire of arguing yet they're still together, so, for her, opposing opinions are not the end of the world, but just a normal thing that is worked out by talking or arguing. You need to trust each other in discussing things and know that there's something unbreakable that links you two even if you don't agree.
For too long, she has not shared enough of her thoughts with me. I think she's not sharing (instead of simply not having any opinions) because there are a lot of simple or complex things that I only find out when I directly ask her about it.
This resonates with me a lot as well. I'm really... succinct, so to speak, and I always think that my thoughts or opinion are clearer to others than they really are. This is not easy to change, because apparently I become fully understandable when to my eyes I'm insufferably verbose. Again, I've learned all this thanks to my SO, that remembers me that she's not in my head.
As for the things you can do after having talked about all this:
Don't stop asking things to her. It shows how much you're interested in what she thinks. However, since she lacks self-confidence, avoid saying things like "Why didn't you tell me before?!" that could have the unintended effect of making her clam up even more. Lean on the side of positive reinforcement instead: "Thank you for telling me this".
You could challenge your wife to express something "superfluous" every day. Make it a game between the two of you.
If anything, exceed in tact and consideration with her.
If it happens that her way of thinking makes you reconsider a decision, tell her profusely. She may not realize that an additional opinion is actually important.
Last but not least:
This situation is not just about her place in the couple. By not "taking her place" in the relationship, she forces you to take the role of couple manager.
You know those people in a couple that won't do anything unless asked and act all surprised when they get reprimanded because they didn't know that the house ran out of eggs, the dog hasn't been brought to the park yet etc? Or the people that when asked about what they want to eat they just say "I don't know, you decide"? Their problem is that they don't consider managing as a work. If you have to take decisions for the couple all by yourself, you're charged with extra stress that should be evenly distributed on both of you. She may not realize this, especially if she thinks that her opinions are just a bother. I think this is a valid point to discuss, maybe not in the immediate time to come. I realize this is a sensitive topic, so ultimately it is up to you to decide to discuss it or try to solve it implicitly.