In my opinion, I think there is no such “disadvantage” with the first method. The first method provides a convenient way to manage the sites, while the second method provides a more secure and feasible way to manage the sites. Which method to be adopted is dependent on your requirement.

There are some scenarios when we need to use a dedicated application pool:
l To separate authenticated content  from anonymous content.
l To isolate applications that store passwords for and interact with external business applications (for example, Business Data Catalog connections).
l To isolate applications where users have great liberty to create and administer sites and to collaborate on content.

There are some references to help  you plan the infrastructure of the SharePoint,
sharepointmagazine.net/.../best-practices-of-sharepoint-farm-configuring-and-deployment-part-1-architectural-and-logical-planning
technet.microsoft.com/en-us/library/cc261834.aspx
Hope this helps.

The disadvantage of option A is that you haven't got a separate authoring environment.
* So say you've got a custom component that you want to deploy and you want to see what that would look like with live content  on it on your authoring farm. In the case of just one web  application it would be visible to your anonymous users right away as there is nog approval on custom development that's either deployed to the server or it isn't.
* Also, as soon as your content is approved  it's live data. You can't setup a content deployment schedule as there is nothing to deploy your content to. It's already there. As soon as the content is approved it's available to anonymous users. And content will be approved per page. So if you were making a lot changes to your site  and you want to launch the new content say July 1st that would be difficult. If you would be using 2 farms you could easily achieve that using a content deployment job that would deploy all approved changes to all pages at the same time.