Can short selling affect my long-term investing account or holdings?

No, short selling does not have an effect on your long-term positions, as it is a separate trade entirely.

What happens if I forget to square off a short sell position?

Short selling must be squared off by 3:20 pm. Otherwise, the broker will automatically close your position at the prevailing rate and levy extra charges for the same.

Are dividends or bonuses relevant for intraday short sellers?

Because positions are not carried overnight, dividends, bonuses, and stock splits do not apply to intraday short sellers.

Why are some stocks blocked from short selling even during market hours?

It could be due to low liquidity, high volatility, or any special restriction imposed by the exchange. The list of allowed stocks is revised periodically to prevent excessive speculation and settlement risk.