SD card ACMD42 command
You are right that according to the specification the DAT3 line has a number of uses.

In SD mode it is the fourth data line and in SPI mode it's the chip select signal.  The Physical Layer Simplified Specification Version 4.10 says:


  At power up this line has a 50KOhm pull up enabled in the card.


And goes on to say (emphasis mine):


  For Card detection, the host detects that the line is pulled high. This pull-up should be disconnected by the user, during regular data transfer, with SET_CLR_CARD_DETECT (ACMD42) command


So the specification explicitly states that ACMD42 should be used to disconnect the pull up resistor.

What would happen if the host doesn't do this?  There are three scenarios:


In 1 wire SD mode this pin is (probably) unused, so maybe it would make no difference.
In 4 wire SD mode this will be a data line, so whatever is driving the bus will need to overcome the 50k pull up.  Maybe this would be a problem at high speed.
In SPI mode this is the chip select pin.  You are unlikely to run into problems toggling it at the speeds involved.


I can only guess about SD mode as that part of the specification isn't public.

Note that a large amount of online code for SD cards is fairly poor quality.  There are various parts of the specification that are quite clear about what a host must do at various points.  These are typically simplified away in public code.  However this code will still work 90% of the time.

So in summary: the specification says you should disconnect the resistor but if you don't you probably won't run into problems in SPI mode.