…ost.

TL;DR Ninja can still stunlock, but for a shorter amount of time and higher energy cost.  Each stun applied is 1 second, with a 1 second cool down.  The ninja may stun 5 times on one small-capacity powercell, for a total of a maximum 5 second stunlock if they use all the energy in their cell.

There is a conflict in the design of ninja stunlocking with their gloves.

Content.Server/Ninja/Systems/StunProviderSystem.cs
Has a comment:

// short cooldown to prevent instant stunlocking
        _useDelay.SetLength((uid, useDelay), comp.Cooldown, id: comp.DelayId);
        _useDelay.TryResetDelay((uid, useDelay), id: comp.DelayId);

However, 
Content.Shared/Ninja/Components/StunProviderComponent.cs
has the following code:

/// <summary>
    /// Time that someone is stunned for, stacks if done multiple times.
    /// </summary>
    [DataField]
    public TimeSpan StunTime = TimeSpan.FromSeconds(5);

    /// <summary>
    /// How long stunning is disabled after stunning something.
    /// </summary>
    [DataField]
    public TimeSpan Cooldown = TimeSpan.FromSeconds(2);

Currently, a ninja may apply a 5 second stun every 2 seconds, and may do this 10 times on a full small capacity energy cell.  This requires too little skill and energy to be considered balanced, considering the ninja's entire toolkit.  

The PR adjusts the stun length to 1 second with a 1 second cooldown, and doubles the energy cost of stunning.  Stunlocking is now still possible, but the ninja can only stunlock for a maximum of 5 seconds and must consume all energy in a small capacity powercell to do so.  This will incentivize ninjas to find other ways of dealing with threats such as crafting cable cuffs or upgrade their suit cell.

referencing Content.Shared/Cuffs/Components/HandcuffComponent.cs

/// <summary>
    ///     The time it takes to cuff an entity.
    /// </summary>
    [DataField, ViewVariables(VVAccess.ReadWrite)]
    public float CuffTime = 3.5f;

    /// <summary>
    ///     If an entity being cuffed is stunned, this amount of time is subtracted from the time it takes to add/remove their cuffs.
    /// </summary>
    [DataField, ViewVariables(VVAccess.ReadWrite)]
    public float StunBonus = 2f;

Stun length was increased to allow ninja to cuff stunlocked targets, making use of the stun bonus.

Each stun now consumes 1/6 of small capacity of powercell instead of 1/5.

The earlier 2.5 second stun and 2.5 cooldown was functional in playtesting, but in response to feedback, a 3 second stun and a 2.8 second cooldown will provide better QoL and account for ping more generously.

Two consecutive stuns is now the same duration as being stamcrit by a stunbaton/disabler etc.

Comment now accurately describes new cost proportional to small, medium, and high capacity powercells.