Is it a bad idea to replace pull-up resistors with hard pull-ups?
The idea of pull-up / pull-down a signal is that the signal is being pulled high or pulled down low most of the time, but can sometimes be pulled down or pulled high respectively.

In the case you want to pull down a signal incidentally that is pulled up most of the time, you want to use a pull-up resistor to prevent huge current drawn from the supply.

So, if your circuit really uses pull-up or pull-down resistors as described above, don't remove them. (For example, when a pin is open collector.)
If in your circuit a signal needs to high or low forever (when the supply is present) and no other component can change the state of this signal, then you can hard-wire it.  Those signal are not called pulled-up, but high, and, respectively not called pulled-down, but low.