You can iterate over your "List of Assets" and check for each asset if it has the software(s) installed with the action "List of Softwares Present in Assets." Another option is using the Action "List of Assets with Specific Software Installed," filling in the Software name and Publisher of the desired software. That gives you a list of assets with that Software installed, but if you want to know the assets "without" that Software, you will need to remove that result from your total number of assets.
Deploying software is possible with Flow builder by integrating with a deployment software tool, such as Intune or PDQ. However, it is not possible to use the on-prem deployment packages, if that's what you mean.
You can also configure your workflow to be triggered every day. So if the workflow successfully deploys a package, it won't deploy that package to the same asset again the next time it runs.