pages do not appear in the dropdown menu if there’s nothing on the pages that can be ordered because the time(s)/date(s) set for the items when they are available is outside the current time/date. that’s intentional.

however, you have chosen to not only display the items not available (that’s optional of course – under the options tab of the plugin), but have also overridden the css to actually allow ordering of the item.
that kind of defeats the point of using the plugin.

I guess I could add an option to NOT remove the pages from a menu if they are empty (i.e there’s nothing on there to order) but am somewhat puzzled why you would use the plugin in the first place ?!

perhaps I am missing something ?

PS: Btw, this has nothing to do with or is caused by the theme you are using with the plugin…

first of all i would suggest, not to use a plugin to do something it’s not meant for.
there is even a very good chance that the plugin will be amended – at some point in the not too distant future – so that you won’t even be able to add things to the cart outside the set hours EVEN IF you remove the covering div ! (After all, that’s the point of the exercise)

secondly – although i do not 100% know what the exact requirements for your site are of course – it seems to me you are listing the menues of different restaurants. if that is the case, i sincerely hope you are using a mutlisite setup (if nothing else at least for your own sanity)

if so, you could simply (staying with bud-alleys here for example) create 3 sites for it (breakfast/lunch/dinner) and make the opening times and menues as required (i.e breakfast has breakfast products and breakfast opening times etc )

then you could use the preorder plugin to actually open the shop but people need to choose an appropriate time in the future if it’s closed.

however, if you are trying to be a “middleman” so to speak , the only half way sensible way i can see is simply adding something to the pages (as you have done) or indeed into the title of each menu item

again though, those are just ideas. i know nothing about the requirements or how all these restaurants work there or what the site is supposed to enable/do

you could also remove this filter in the plugin
add_filter('wp_get_nav_menu_items', array($this,'wppizza_tm_exclude_nav_menu'), null, 3 );/*exclude posts and pages from nav menu (appearance->menus)*/

via some remove_filter class

but – as mentioned above – this might not help you in the long run anyway (unless you will never update the plugin )

what shortcode ?
i did no say anything about shortcodes..

>pickup and deliver the food to the customer, nothing to do with the actual restaurant.
none of my business of course, but I am wondering what the site does if the restaurant in question is closed…..just thinking out loud though.

removing that filter does nothing to the menu layout or css as it does not add anything to it in the first place when used. it simple removes items from the list ….

looks to me more like your menu hierarchy is not what it should be but that is not anything wppizza or any wppizza plugin influences. (but megamenu will probably)