No, the automatic updates will not affect your changes.
Whenever you customize a default SharePoint page (DispForm.aspx in your case), it becomes unghosted and the changes you made to the page are stored in the Content database. Now whenever you make a request to that page, the data from both the file system (original page) and the content database (custom changes) is fetched and shown.
Also as a result of unghosting, if you modify any particular list's DispForm.aspx, then the changes are reflected only on that list and not every other list's DispForm.aspx.
This does not directly answer your question, but:
If you use
<CustomAction Location="ScriptLink" /> in a Module and deploy that and try writing selectors that don't depend on ID you should be safe.