Brightness issues driving 10*11 SMD 5050 LEDs matrix
Any LED multiplexing solution will inherently reduce intensity of the LEDs pretty much linearly by the factor of the multiplexing duty cycle. This change in intensity is not identical to the change in intensity observed when current through the LED is reduced by changing series resistance: The resistance value is not directly the determining factor, the resultant current through the LED is, and that does not enjoy a linear relationship to resistance.

The human eye's perception of intensity of light, LED or otherwise, is far from linear: Intensity variations at low LED intensity, or for that matter in low ambient light conditions, are much more sharply perceived, than a similar change in intensity at a brighter point in the intensity curve, or under brighter ambient light conditions. This explains why the change in resistors did not show a significant change in perceived intensity.

To answer the specific question about over-driving LEDs: Yes, that is a standard mechanism for countering loss of intensity in multiplexed displays. To counter a 8-way multiplexed LED display's intensity drop, i.e. 12.5% duty cycle per LED, hypothetically the LED should be driven at 8 times the constant current. However, that is rarely practical, so either compromises must be made, or risks of LED damage must be accepted. 

How much a given LED can be safely overdriven by, is (a) possibly specified in the datasheet, but (b) more typically determined by the display designer through empirical testing, especially in hobby and low-cost applications, if the datasheet-specified overdrive current is not sufficient, and risk of LED failure is acceptable. 


For more context on LED overdriving limits for pulsed load, see this answer.
For a more detailed description of LED intensity and human perception, see this answer.
Another answer in the same vein, with pretty graphs too.