Would the Apple store be able to remove malicious software and viruses from iPhone?

If such a thing existed, I’m sure they could…

However, there are no known viruses in the wild that can infect an iphone that has not been jailbroken.

If you suspect the device has been compromised, force it into recovery mode and restore ios, then set it up as a new device. (Do not restore a backup you suspect may be compromised).

iOS / iPadOS devices cannot be infected** with Viruses / Malware / Spyware unless you have intentionally downloaded spurious software or unauthorized apps directly from the internet and installed them on your device or/and have Jailbroken. 

**The primary reason for this is Sandboxing. All third-party apps are “sandboxed”, so they are restricted from accessing files stored by other apps or from making changes to the device. Sandboxing is designed to prevent apps from gathering or modifying information stored by other apps.

Security of runtime process in iOS and iPadOS - Apple Support

The sandbox on an iPhone is a security feature that creates a restricted environment for each app to run in isolation from other apps and the operating system. It is a core component of iOS's security architecture and plays a crucial role in making iPhones more secure.

In layman's terms:

The sandbox works by enforcing strict controls and limitations on app behavior, ensuring that each app has access only to the resources it needs to function properly. Here are some key aspects of the sandbox that contribute to iPhone security:

1. Isolation: Each app on an iPhone operates within its own sandboxed environment, which means it has no direct access to the files, processes, or memory of other apps. This isolation prevents apps from interfering with one another, protecting user data and maintaining system stability.
2. Restricted Resource Access: The sandbox restricts an app's access to sensitive resources such as contacts, photos, location data, and system settings. Apps must explicitly request user permission to access these resources, and users have control over granting or denying access. This helps prevent unauthorized data access and ensures user privacy.
3. Limited File System Access: Apps can only access their own containerized storage area and specific system-provided directories. They cannot modify files outside of their designated areas or interfere with the operating system files. This prevents apps from tampering with critical system components.
4. Code Execution Controls: The sandbox enforces restrictions on code execution, preventing apps from running arbitrary code or injecting malicious code into other apps or the system. It helps ensure that apps only execute approved code from their own sandboxed environment.
5. App Review Process: Before an app is allowed on the App Store, it goes through a rigorous review process conducted by Apple. This review examines the app's functionality, security, and adherence to guidelines. It helps detect and remove malicious or poorly designed apps, minimizing the risk to users.

The combination of these sandboxing mechanisms helps create a secure environment on iPhones, protecting user data, maintaining system integrity, and preventing unauthorized access or interference between apps.