Example:
Values: 1000, 2000
Combinations: 01-1000-00, 01-2000-00

Affect of Disabling a Segment Value:
Once you disable a segment value, lets say 1000, you will not be able to use the value 1000 in any new data entry, be it a journal entry screen or invoice line screen or purchase order screen.

Significance of Combination Being Enabled:
As long as the combination is enabled, the existing data will keep on flowing internally. For example if you a requisition touching the combination 01-1000-00, you will be able to create a purchase order.
If you have a purchase order touching this combination you will be able to create an invoice. If you have an invoice using this combination, you will be able to create accounting. If you have a journal line using this disabled combination, you will be able to post it.

I hope this clarifies the significance of enabling/disabling the values and combinations.

Having said that one can keep the statuses of values and combinations in synch by running Segment Value Inheritance program. However if you decide to disable combinations as well along with the values you must make sure nothing would get stuck in the pipeline (as explained above).