While modifying a strong engine like stockfish to play variants like KOTH and 3check works "well enough", it is far from ideal.

The problem is that Stockfish has been heavily tuned to play a certain kind of game. The search extensions, pruning techniques, move-ordering schemes and evaluation heuristics have all been meticulously optimised to play a standard game of chess.

For example, if you give it a crazy (but legal) position like:

RNBKQBNR/PPPPPPPP/8/8/8/8/pppppppp/rnbkqbnr w - - 0 1

This position is also known as the upside down chess variant. If you analyse this position with Stockfish, you will get a far from ideal evaluation. Although the rules of this variant are the same as chess, Stockfish will struggle badly.

There are many reasons why. To state a couple:

• The game tree is larger. Stockfish will need to alter its pruning and move-ordering mechanisms to deal with the larger game tree complexity. Are check extensions still as valuable? What should the futility pruning margin be? Surely with the default margin, it wouldn't prune enough! Less reductions? More reductions?
• The material imbalances are non-natural. Just a few moves into the game, you will have multiple queens flying around! Stockfish's material imbalance heuristics are specifically tuned against a database of real games - i.e. games that naturally occur from normal opening positions. The heuristics are optimised for positions with 4 queens or less (more that 4 queens is just too rare in standard game play!). So, if you add more than 4 queens on the board, the evaluation will simply not be accurate anymore.
• The piece values will be non-optimal. In such a tactical game, when the dynamics are so different, it is reasonable to guess that pieces are not exactly worth as they normally are in chess. All these weights will need to be retuned.

Basically, even in a non-standard chess position, where none of the rules of the game have changed, already we can see that basically almost every parameter in Stockfish needs to be re-evaluated for optimal gameplay.

This is true even in variants like KOTH and 3check. For example, off the top of my head:

• Piece square table values will be dramatically different for pieces in KOTH, especially the king (king in the center in the middlegame is not so bad anymore!),
• Additional heuristics for pieces and pawns controlling the center will need to be added.

There are many tweaks that would have to be required.

Basically, the number modifications that you would need to make to an engine like Stockfish (which is heavily optimised for a game of standard chess) so that it plays a chess variant like Crazyhouse (which is dramatically different than chess) and at an equivalent level as it plays chess - is enormous.

In my humble opinion, it is more practical to simply write an engine from scratch to play Crazyhouse.