Not a bug
BYOND Version:515.1603
Operating System:Windows 11 Pro
Web Browser:Chrome
Applies to:Dream Maker
Status: Not a bug

This is not a bug. It may be an incorrect use of syntax or a limitation in the software. For further discussion on the matter, please consult the BYOND forums.
Descriptive Problem Summary:
The map editor does not allow you to remove objects using SHIFT+Click as it did before.

Numbered Steps to Reproduce Problem:
Attempt to remove any object using SHIFT+Click to quickly delete it from under your cursor.

Expected Results:
The object is not deleted. The default behavior for your selected tool is performed.

Actual Results:
Object is deleted.

Lummox JR resolved issue (Not a bug)
This was an intentional change. Shift and Ctrl now affect pixel placement.
What is the new hotkey to delete objects?
There isn't a delete modifier anymore. The modifier keys have been changed completely. For deletion you'd want to either undo, or switch to the erase mode.
Would it be possible to provide a mode to erase all atoms of a specific type? Having to set each object as active in order to erase them is very cumbersome.
In response to Crazah
Isn't there find and replace? Replace it with an empty string and they're deleted.
In response to NSBR
That is also very cumbersome compared to the old functionality.
In response to Crazah
True. Just giving you a workaround.
Bumping and rewriting the feedback about this part of the rework:

It was previously possible to delete topmost objects using SHIFT modifier.
It still works like that in "Fill Rectangle" mode, but only for the selected object type. Convenient for small changes, but is absolute nightmare when designing and redesigning large and highly detailed maps.

How to fix and improve:
1) Fill Rectangle with SHIFT modifier should delete topmost objects.

2) Leave "per object type" behavior to the Eraser Tool. Eraser Tool should always work on an area like Fill Rectangle instead of the current one deletion per click behavior to allow for easy deletion of objects of the specific type.

3) INS/REP toggle should affect all selected types of atoms instead of turfs only. So it would be possible to replace a room full of furniture with another room with furniture using copy-pasting or dragging of a selected area. Such simple action is impossible in 515.

4) INS/REP toggle should be respected when placing objects and replace all objects on a turf like it worked by default in 514. That way you are confident that you're not placing the same object twice, and also have an option of quickly replacing a table with many items on it with some other object.

I hope that I worded it better this time. These suggestions combined should restore the previous functionality without taking anything from the recently added features and behaviors.
That's really more in the realm of a feature request rather than a comment on a closed bug report. Plus you have several items in that list that are actually quite separate, like the INS/REP toggle behavior. (Changing INS/REP for non-turfs doesn't really make sense, though.)