I think an important thing to understand and realize is the feelings you have for this situation. You say that your girlfriend makes you worried given her recent behavioral developments; she does things that concern you about the health of the relationship.
The messages that you noticed are just another behavior she's exhibited that you found you do not like. I propose that rather than addressing one thing specifically, you talk to her about everything you've felt.
There's a few things you might want to note about your situation as I understand it:
- It seems like there's a lack of trust in both directions
- Communication seems to be less than ideal
- Little understanding of entirety of situation
You'll need to address these issues to have a more stable and healthy relationship by talking to her about how you felt in response to things she's done before.
Realize that constantly confronting her about who she messages or talks to is only going to make you look insecure and controlling; subsequently making her defensive of the situation. If you don't like who she talks to or sees, you can tell her how you feel about them and then make the decision of whether or not the relationship is worth continuing.
Those behaviors she's showing that you don't like are only part of the problem. There's a much more concerning root problem: lack of trust and understanding of each other.
For the foreseeable future: start establishing trust, openness, and a good communication channel. You'll find that when you're both on the same page you'll be less likely to encounter problems like this.
How can I bring the topic on the table and make her confess . . .
You can't "make" anyone confess. Also consider how you're prejudging her by looking at it as a "confession". How do you know she's actually done something wrong yet with these guys? Go into your conversation with open eyes. Don't form any conclusions until you've discussed the issue with her.
. . . and understanding what's going on...inducing in her the feeling that I know about it, but without saying (and without making her understand) that I read the messages?
You're making this too complicated. It really is as simple as telling her how you feel about the messages in general. Don't be specific and accusatory. Just tell her something like:
Hey love, I've noticed you talking with other guys lately and it worries me there might be something wrong between us. Am I wrong to feel this?
Focus on the topic of how you feel. Tell her it worries you with all the men she's talking to and how you're concerned about the relationship. Don't tell her she can't do it or she's wrong for doing so, that'll only make her more upset since you're attempting to control her behavior.