With one site per function, one can achieve simple security, clearly show the purpose of that site, and clearly show who owns the content. All this makes tracking easy. SharePoint doesn't automatically add navigation for new site collections, only sub-sites. Each site collection is its own secured silo. The site doesn't exist until you make it visible through navigation.
Modern SharePoint Sites does not support Master Page, though there is limited ability to brand on Modern sites. Themes with simple colours, headers, and footers can be customized, but it is not as flexible as Classic Sites. One of the main advantages of Modern Sites is the accessibility of online, on the go content that is both usable and legible on all devices. Unlike Classic Sites, Modern Sites naturally rearrange to fit onto the device screen. Gone are the tiny words and lines along with the impossible buttons to push. Instead, readable text and a user interface that provides links and buttons that one can use without a micro-sized finger. Microsoft’s decision to remove Master Page and retain full control over the UI guarantees that SharePoint online will show and maintain a consistent, visually pleasant, and usable mobile experience.
With SharePoint Classic Sites, it was common to inject the pages, including the Master Page, with scripts to customize for branding and looks. However, this practice was not supported by Microsoft and could result in the loss of functionality within SharePoint after upgrades and releases. Realizing that many companies require a methodology to brand and customize, Microsoft has provided SharePoint Framework web parts and design patterns. Framework allows the same type of functionality as script injection; however, it provides control and organization around it. SPFx Application Customizer provides access to well-known locations on SharePoint pages that you can modify based on your business and functional requirements. Once again, it maintains its mobile-first advantages. It is important to note that, technically, if a customer truly wanted to customize their Modern Site, it could be done but this could result in breaks in other areas of SharePoint and/or with future additions and upgrades.
So, coming back to the original question: should one stay with SharePoint Classic Sites or switch to SharePoint Modern Sites? Since SharePoint Modern Sites is focused on having content at your fingertips, whether you are in your office or on the go with your mobile phone, a consideration to migrate or not is to factor in how important it is to your corporation for mobile access. If it is high on the priority list, then migrating to SharePoint Modern Sites is advisable.
Can you have both? Yes, you can migrate to SharePoint Modern Sites and toggle to Classic Sites, but it is important to ask whether your users will be appreciative of the different feel and inconsistency between the two sites. Sometimes, it is better to commit to one side of the fence than sitting on it, as it is in this case, as the inconsistency may result in confusion for your users.
When we consider and review the Road Map for SharePoint and Office 365, it is clear Microsoft will continue on the road for mobile applications that provide super responsive content while on the go with out of the box, ready to use while being easily customizable for content. It is also noted that new features, web parts and enhancements will be made on the modern SharePoint, where classic will stay as is without any further enhancements. Eventually, the decision will have to be made to migrate to SharePoint Modern Sites, but there is time as Modern Sites is still in its infancy. Until then, keep in mind the architecture, the Road Map, and the targets as you design your corporation’s infrastructure for SharePoint and Office 365.