MSP430 USCI - Are the interrupt flags still active when interrupts are explicitly disabled
Yes. That is how polled data transmissions are implemented.

Interrupt flags are independent from interrupt enables. IFG bits are set when specific hardware conditions are met and may trigger interrupt when associated IE bit is also set. Procedure for clearing the flag is the same for both cases.

There might be an exception when the flag triggers a DMA transfer, in that case the flag is cleared automatically.