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I'm in the process of designing a device capable of charging, discharging and testing internal resistance of 18650 cells. My device will be capable of testing 100x 18650 at the same time, each will have their dedicated module which allows them to run independent from one another.

The pre-designed modules are capable of charging and discharging at 1A however they also have a feature which throttles and reduces the wattage when the battery becomes too hot. This feature is important as this will help answer my question at the end.

In the charging phase of the test they are only charged at around 250ma as this helps to find cells with internal problems and cause the cell to run hot, so no throttling will occur.

During the discharge phase however I need to test the cells at 1A discharge but often the modules will throttle because the battery is getting warm/hot.

I've read comments, forums and even articles saying you should not cool lithium batteries since they cook inside or they change the chemistry within the battery, but I'm unable to find any reputable information that could be considered fact, I know that many electric cars have air ducts to help cool the battery but this doesn't mean its good for the batteries? I'm really unsure and confused.

Is there any scientific reason why you should NOT blow air across batteries while in use or during a charge cycle?

Tesla 18650 batteries are cooled by propylene glycol coolant in a heat exchanger system.

See, for example, US20140178722A1 and US 8,758,924

Some more information on Tesla's particular implementation here.

Your concern is somewhat misplaced. At 1 A charge-discharge, normal 18650 Li-Ion batteries do not heat up. Consider that normal battery heats up only due to Joule dissipation over ESR, and the ESR of most 18650 cell is under 100-150 mOhms. So the maximum internal dissipation is under 200 mW, which, for the physical size (and surface area) of 18650 cell is nearly nothing.

However, since you plan to discharge them, you will have full 4 W dissipation in each of your loads, so a fan blower will be a must.

Car batteries gets discharged (and charged during recuperative braking) at much-much higher rates, and only then the internal dissipation/heat generation becomes an issue.