> Can I still program the ESP32-S3 via the D+/D- pins ?
Probably - you'll need to hold BOOT/IO0 down while resetting the chip to enter download mode.

You've connected the programming header to the USB D+ and D- pins, not UART ie serial. The UART pins are GPIO43/44 which are probably what you're after. The data sheet recommends capacitors on EN and BOOT, but it won't stop it being programmed / seeing some output. I wouldn't tie unused pins to grou...