There are a lot of techniques, but in the end it all boils down to reading the other person's mind.

For example, then used Intelligence, you might get an information about spies enemy player operate, especially about layout of spies.

But it's not always clear why enemy specified that layout.
In the first place, there is no guarantee that a friendly Spy can always obtain an enemy Spy's layout by fraud.

Also, even if all the information is obtained, even if the enemy tries to show all the hands, the information will be different from the plan that the enemy was trying to realize.
The spy extracts one aspect of the situation where the plan is progressing to some extent as planned, but part of it is broken due to lack of control.
So the ability to analyze information obtained by spies will be very important.

And the ability to derive reasonable solutions from the analysis results, realize and implement them is also important, although it has a lower priority than the analysis of information.
For example, an enemy may destroy your goods because they don't want you to invest in something else.
If this guess is wrong, even if the subsequent action is not useless, only a low effect can be obtained, so the priority is inferior ( In actual play, please think more abstractly, such as "some purpose for destroying my goods", and please expose many potentialities ).
Even at this point, there are several strategies that can be considered in the abstract.

For example, if the main goal of the enemy is the destruction of your own country, you will need to resist thoroughly, but if enemy plan to continue using you from the beginning until the end of the game, there is a high possibility that you should be able to build a mutually beneficial relationship without control.
And, if there are explicit or implicit conditions for enemy, then you satisfy the requirements, they might still be able to build a mutually beneficial relationship.

Please collect information using spies and more.
And think about how you will use the information you collect.

Abstractly, induce a situation where the enemy wants to stop destroying the goods.
However, the specific steps should be case-by-case.

For example, it might be possible to have a strategy of becoming an ally though.
However, it might be necessary to carefully analyze whether the enemy has the same interests or whether the relationship will change due to changes in the situation.

Even if you choose another scenario based on another strategy, the specific content may be different, but the branching always occur as described above.
So it's "case by case".

Just put one in every core city. There are only 5. The rest are not worth attacking or defending.

wiki.callofwar.com/wiki/ESPIONAGE#Spies
The URL above says:
" ( Buildings ) Also has a chance to reveal a momentary snapshot all armies in the target province as well as in adjacent provinces, including armies of other nations present in these provinces. "

Therefore, you are wrong.
If you choose to strategy that prevent resource destruction by arresting enemy spies, placing a Counter Espionage "in the target province" where the enemy spies are located has a higher chance of success.

And if possible, please consider cost performance.
Also, it would be better to regard performance in two dimensions: economic and military or political.
In other words, the enemy is destroying the goods, but if the value of the goods is low, it is okay to be destroyed them until the enemy is satisfied.
However for example, if the current market value of goods to money is 1 to 30, it will be a big loss economically.
Or if Infantry, Ordnance, Aircraft, etc., which require goods for production and maintenance, are valuable as a presence against hostile forces, it will be a big loss also.

And if enemy was strong, it is no choice that compromise the budget for counterintelligence exceed the cost of enemy intelligence, but it must not exceed the loss of case of no counterintelligence at all.

The original question was about resource destruction (economic sabotage).
Resources can be destroyed only where they are produced.
And very few cities+provinces produce a meaningful amount of goods.
Your core cities and core resource provinces, that's it.
Nothing else is worth talking about.

Military sabotage is a different topic.
Can you stop spies from stealing your plans?
Maybe, if you cover your whole country with structures and/or spies.
As we all know, spies reveal plans if 3 (or more) of them perform military sabotage in an empty province.
So, you can use counter-spies, or you can build a structure in every province.
That's too expensive to be a realistic approach.

In order not to place spies in all provinces, it is rather necessary to find out the opponent's intentions.
Also, it was suggested that the thread starter thought that not only the first question, but also subsequent questions could be resolved in a makeshift way, so I explained what was actually happening behind the situation.

The enemy does not destroy goods for the sake of destroying goods.
Destroy goods to fulfill some intention.

Near the end of day start construction on expensive buildings so that you have as close to zero resources in the bank.
After the day change, cancel all the buildings.

It's kind of fun to see what combo of industry, ports, intra, bunkers, etc is the best for your situation.

Just so you know, canceling a build returns ONE HALF of the remaining (unspent) resources. Starting and canceling will waste half of your resources, every night. The self-inflicted damage is worse than anything the enemy can do to you with spies. It's literally the worst possible thing you can do in the game

Is that confirmed, I thought all unused resources get returned?

Yes, all resources are returned when you cancel a build, except when you let it run for a while and a partial building is constructed; in that case, it is proportional.

Thanks for the correction, I must have been observing the effect of partial builds.

Same strategy can you used if you are gonna lose a core resource city.

Or you can just give it to ally and take it back afterwards

As far as I know the looting of ressouces will not affect you directly. Only the conqueror will have a bonus.