There are various reasons in favor of plugging the port when placing a high-pass filter on a small ported speaker. There isn't much downside. As you point out, the woofer isn't optimized for use in a sealed enclosure. This would matter with a subwoofer, but not so much with a small speaker. A subwoofer driver intended for use in a ported enclosure isn't going to deliver deep bass when it isn't supplemented by the port (or passive radiator). With a small speaker it likely won't matter; the thing that is more likely to matter is that the enclosure may be larger than is to be desired unless something is done to reduce the interior volume. If nothing is done to reduce the interior volume, the interior volume will be greater than the volume at which the system Q would be .7 or thereabouts. If nothing is done to reduce the interior volume, you end up with a system Q that can be much lower than is suitable, possibly lower than .5. Not even this will necessarily be a problem, however the potential effect is that the bass rolloff, which will be unusually shallow, will start at higher frequency. You could potentially notice a slight loss of SPL in upper bass. If so, this is correctable by doing something to reduce the interior volume, but this would likely involve some experimentation. The practical solution is to block the port at its inner end, so that the volume of the port itself does not end up being added to the enclosure volume. For someone not opposed to removing the woofer so as to be able to plug the port at its inner end, this would be the way to do it.
By the way, the rule that is conventionally used to decide the best use for a given driver is based on the ratio of Fs to the electromotive portion of the damping (Qes). It is actually better to base it on Fs/Qts. This ratio practically determines the theoretical F3 for a sealed enclosure. For a driver to work well in a sealed enclosure, and produce adequately deep bass, this ratio ideally needs to be less than roughly 50. For a driver to take best advantage of the port in a ported enclosure, this ratio needs to be greater than roughly 100. Often it is said that drivers with this ratio falling in the middle, between 50 and 100, can be used for either type of enclosure. Perhaps, but this won't be an optimized design. For a sealed enclosure, you can estimate F3 by multiplying this ratio by .73 (this is a good multiplier for Qtc values in the typical range from about .65 to .9). For a small speaker that won't be expected to produce deep bass because a subwoofer is used and a high-pass filter is added to the small speaker, the F3 value isn't important, and because the F3 value isn't important, neither is it important for the Fs/Qts ratio to be optimized for sealed enclosure use. All that is going to matter in this case is for the enclosure volume to be small enough to insure that Qtc will be not less than .5. (The conventional school of thought is that Qtc should be about .7, but there are varying opinions.)