IANAL and I'm not intimately familiar with the US legal system but I'm pretty sure the license applies to all code not explicitly covered by any other license, even if it's not added as a file header (otherwise all similar projects in which the license is merely distributed as the LICENSE file and referenced in the README would be unlicensed too). Term 0 actually only says a notice must be placed in the "program or other work" -- placing that notice in the readme seems sufficient if the readme is part of the program/work. The suggestion of how to apply the license is explicitly just a suggestion or recommendation, not a requirement.
The existence of non-GPL plugins without a proper exemption however might be problematic for re-distribution of the bundle in other GPL software. It could be argued that the plugin in question isn't part of the code covered by the GPL but then the official Wordpress distribution itself is obviously also not entirely GPL and can't be redistributed fully under the GPL.
For an example of partially GPL-compatible software re-distributed under GPL consider the program formerly known as IceWeasel: https://en.wikipedia.org/wiki/GNU_IceCat (a modified version of Firefox minus the proprietary branding).
The existence of non-GPL plugins without a proper exemption however might be problematic for re-distribution of the bundle in other GPL software. It could be argued that the plugin in question isn't part of the code covered by the GPL but then the official Wordpress distribution itself is obviously also not entirely GPL and can't be redistributed fully under the GPL.
For an example of partially GPL-compatible software re-distributed under GPL consider the program formerly known as IceWeasel: https://en.wikipedia.org/wiki/GNU_IceCat (a modified version of Firefox minus the proprietary branding).