If appearing on your mobile site, then yes, they may not rank as highly.
Helping users easily access content on mobile
You can see with the examples they give, they don't mention if they are deceitful or malicious, simply that they obscure the content:
Showing a popup that covers the main content, either immediately after the user navigates to a page from the search results, or while they are looking through the page.
Displaying a standalone interstitial that the user has to dismiss
before accessing the main content.
Using a layout where the above-the-fold portion of the page appears
similar to a standalone interstitial, but the original content has
been inlined underneath the fold.
To continue to have a pop up while avioding the penalty, you will need to use small smart style banners, such as the example they give:
Banners that use a reasonable amount of screen space and are easily dismissible. For example, the app install banners provided by Safari and Chrome are examples of banners that use a reasonable amount of screen space.
Although this is only on mobile devices, you can still continue to show them on desktop.
(Until they decide to penalise pop ups on desktop too)