Canon 60Da has a 18.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features Digic 4 processor. On the other hand, Canon 90D has a 33.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features DIGIC 8 processor.
Canon 90D's sensor provides 15MP more than Canon 60Da's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Below you can see the 60Da and 90D sensor size comparison.
Canon 60Da and Canon 90D have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Canon 60Da has 80% larger pixel area compared to Canon 90D, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.