Typing shortcuts in MacOS Sierra
Based on your question, you're probably familiar with much of this process but I'll lay it out from start to finish just in case.

In System Preferences > Keyboard > Text, add an item. On the left, pick a shortcut sequence. On the right, you need to enter the desired character. There are a variety of ways to do this here but one straightforward way to do so would be to Show Emoji and Symbols†, enter the character name (e.g. meteg) in the search field and then double-click on the result‡. This will place the character wherever the cursor would be, which in this case, should be in the 'With' field in the Text preferences.

From within Pages (or TextEdit) enable Edit > Substitutions > Text Replacement. When done, there should be a checkmark beside the option. As far as I can tell, this setting will stick as long as it's a standard Cocoa app.

To use in Pages, open a doc and type the shortcut and hit space (or some punctuation character).

† I have 'Show Input menu in menu bar' checked in the Keyboard > Input Sources preferences so I typically grab the 'symbols' from there. But if you don't have that enabled, and don't want to, you can select 'Emoji &amp; Symbols' from the Edit menu of most standard apps.

‡ Other methods might be to enable the appropriate script in the Symbols and Emojis window, or to paste the character from wherever you might find it.