I don't know the limits off hand, but with that many custom values, I'd store them in a table and refer to them that way if at all possible. That allows you to use database tools to manage the list of values and this will be much less time consuming than doing the same thing with a custom value list.
It also gives you the option of using a conditional value list to produce a more manageable list of values in the drop down by using a second field to specify a subset of the total values in the list.
Will this solution allow a user with very very basic knowledge of FileMaker to update the list on a regular basis? The person who is managing this part of the database basically only knows how to to data entry and perform basic searches, and alter custom value lists by clicking the Edit button at the bottom of the list.
You can add an edit button to the layout that takes the user to a layout where the values are listed fpr editing. You can even pop this up in a floating window. You just click the button, edit the values as needed and then either click a button or close the floating window to return. You can even use a portal so that adding a value is a simple as typing text in the blank bottom row and deleting a value can be controlled with a delete button in the row.
If you want you can give the user a number of managment tools for their value list that aren't possible with custom values such as a check box that temporarily removes a value from the list if checked and you can enable visual spell checking to help catch input errors.
The only thing you really lose is the ability to specify an arbitrary order to the values. Filemaker insists on listing the values in ascending order when you specify a field as the value source.