Did they remove the Golden Apple from Minecraft?

Don't think so. Do you know how to craft it? It is an apple in the center surrounded by gold nuggets

No they didn't. There are two ways to make golden apples. An apple surrounded by golden bars. Or you can make it by surrounding it with gold blocks.

The Golden Apple is still in Minecraft, but crafting recipe has changed over time.

In the current versions, you'll need to surround the apple with 8 gold bars (NOT GOLD NUGGETS, as this was changed around v1.6.1… You'll need to craft the nuggets into bars @ 9:1 ratio, so you'll need 72 nuggets for this) to get the basic Golden Apple.

If you craft if with Gold Blocks instead (again the ratio for bars to blocks is 9:1… So you'll need 72 bars or 648 nuggets to make this), you get the Enchanted Golden Apple… Which adds Fire & Damage resistance to the effects of the regular Golden Apple.

Please be aware that Golden Apples are not considered a wise investment of world resources due to the amount of gold required for them… HOWEVER, Gold is currently a semi-renewable resource (as nuggets can be obtained from killing Zombie Pigmen)… So you won't necessarily run out.